Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.

Science.gov (United States)

Hoenen, Thomas; Groseth, Allison; Rosenke, Kyle; Fischer, Robert J; Hoenen, Andreas; Judson, Seth D; Martellaro, Cynthia; Falzarano, Darryl; Marzi, Andrea; Squires, R Burke; Wollenberg, Kurt R; de Wit, Emmie; Prescott, Joseph; Safronetz, David; van Doremalen, Neeltje; Bushmaker, Trenton; Feldmann, Friederike; McNally, Kristin; Bolay, Fatorma K; Fields, Barry; Sealy, Tara; Rayfield, Mark; Nichol, Stuart T; Zoon, Kathryn C; Massaquoi, Moses; Munster, Vincent J; Feldmann, Heinz

2016-02-01

Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions. We successfully used a novel, pocket-sized nanopore sequencer at a field diagnostic laboratory in Liberia during the current Ebola virus outbreak.

Extracting flat-field images from scene-based image sequences using phase correlation

Energy Technology Data Exchange (ETDEWEB)

Caron, James N., E-mail: Caron@RSImd.com [Research Support Instruments, 4325-B Forbes Boulevard, Lanham, Maryland 20706 (United States); Montes, Marcos J. [Naval Research Laboratory, Code 7231, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States); Obermark, Jerome L. [Naval Research Laboratory, Code 8231, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States)

2016-06-15

Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method uses sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.

Memory and learning with rapid audiovisual sequences

Science.gov (United States)

Keller, Arielle S.; Sekuler, Robert

2015-01-01

We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

Memory and learning with rapid audiovisual sequences.

Science.gov (United States)

Keller, Arielle S; Sekuler, Robert

2015-01-01

We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

An Imaging And Graphics Workstation For Image Sequence Analysis

Science.gov (United States)

Mostafavi, Hassan

1990-01-01

This paper describes an application-specific engineering workstation designed and developed to analyze imagery sequences from a variety of sources. The system combines the software and hardware environment of the modern graphic-oriented workstations with the digital image acquisition, processing and display techniques. The objective is to achieve automation and high throughput for many data reduction tasks involving metric studies of image sequences. The applications of such an automated data reduction tool include analysis of the trajectory and attitude of aircraft, missile, stores and other flying objects in various flight regimes including launch and separation as well as regular flight maneuvers. The workstation can also be used in an on-line or off-line mode to study three-dimensional motion of aircraft models in simulated flight conditions such as wind tunnels. The system's key features are: 1) Acquisition and storage of image sequences by digitizing real-time video or frames from a film strip; 2) computer-controlled movie loop playback, slow motion and freeze frame display combined with digital image sharpening, noise reduction, contrast enhancement and interactive image magnification; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored image sequence; 4) automatic and manual field-of-view and spatial calibration; 5) image sequence data base generation and management, including the measurement data products; 6) off-line analysis software for trajectory plotting and statistical analysis; 7) model-based estimation and tracking of object attitude angles; and 8) interface to a variety of video players and film transport sub-systems.

Failed rapid sequence induction in an achondroplastic dwarf

Directory of Open Access Journals (Sweden)

Jasleen Kaur

2011-01-01

Full Text Available Achondroplasia, a common cause of short limbed type of dwarfism is due to quantitative decrease in rate of endochondral ossification. This abnormal bone growth leads to disproportionate body and head structure, thus placing them under high risk for anaesthetic management. There is paucity in literatures, regarding appropriate drug dosage selection in these patients. Use of drugs as per standard dosage recommendations based on body weight or body surface area, may not be adequate in these patients owing to discrepancies in overall body weight and lean body weight, especially during rapid sequence induction. Here, we report a case of failed rapid sequence induction due to abnormal response to administered drugs in an adult achondroplastic dwarf. Standard doses of thiopentone and rocuronium had to be repeated thrice to achieve adequate conditions for intubation.

Spatio-temporal alignment of pedobarographic image sequences.

Science.gov (United States)

Oliveira, Francisco P M; Sousa, Andreia; Santos, Rubim; Tavares, João Manuel R S

2011-07-01

This article presents a methodology to align plantar pressure image sequences simultaneously in time and space. The spatial position and orientation of a foot in a sequence are changed to match the foot represented in a second sequence. Simultaneously with the spatial alignment, the temporal scale of the first sequence is transformed with the aim of synchronizing the two input footsteps. Consequently, the spatial correspondence of the foot regions along the sequences as well as the temporal synchronizing is automatically attained, making the study easier and more straightforward. In terms of spatial alignment, the methodology can use one of four possible geometric transformation models: rigid, similarity, affine, or projective. In the temporal alignment, a polynomial transformation up to the 4th degree can be adopted in order to model linear and curved time behaviors. Suitable geometric and temporal transformations are found by minimizing the mean squared error (MSE) between the input sequences. The methodology was tested on a set of real image sequences acquired from a common pedobarographic device. When used in experimental cases generated by applying geometric and temporal control transformations, the methodology revealed high accuracy. In addition, the intra-subject alignment tests from real plantar pressure image sequences showed that the curved temporal models produced better MSE results (P alignment of pedobarographic image data, since previous methods can only be applied on static images.

MISTICA: Minimum Spanning Tree-Based Coarse Image Alignment for Microscopy Image Sequences.

Science.gov (United States)

Ray, Nilanjan; McArdle, Sara; Ley, Klaus; Acton, Scott T

2016-11-01

Registration of an in vivo microscopy image sequence is necessary in many significant studies, including studies of atherosclerosis in large arteries and the heart. Significant cardiac and respiratory motion of the living subject, occasional spells of focal plane changes, drift in the field of view, and long image sequences are the principal roadblocks. The first step in such a registration process is the removal of translational and rotational motion. Next, a deformable registration can be performed. The focus of our study here is to remove the translation and/or rigid body motion that we refer to here as coarse alignment. The existing techniques for coarse alignment are unable to accommodate long sequences often consisting of periods of poor quality images (as quantified by a suitable perceptual measure). Many existing methods require the user to select an anchor image to which other images are registered. We propose a novel method for coarse image sequence alignment based on minimum weighted spanning trees (MISTICA) that overcomes these difficulties. The principal idea behind MISTICA is to reorder the images in shorter sequences, to demote nonconforming or poor quality images in the registration process, and to mitigate the error propagation. The anchor image is selected automatically making MISTICA completely automated. MISTICA is computationally efficient. It has a single tuning parameter that determines graph width, which can also be eliminated by the way of additional computation. MISTICA outperforms existing alignment methods when applied to microscopy image sequences of mouse arteries.

Image registration method for medical image sequences

Science.gov (United States)

Gee, Timothy F.; Goddard, James S.

2013-03-26

Image registration of low contrast image sequences is provided. In one aspect, a desired region of an image is automatically segmented and only the desired region is registered. Active contours and adaptive thresholding of intensity or edge information may be used to segment the desired regions. A transform function is defined to register the segmented region, and sub-pixel information may be determined using one or more interpolation methods.

Minimum TE gradient-recalled phosphorus imaging sequence on a whole-body imager

International Nuclear Information System (INIS)

Listerud, J.; Lenkinski, R.E.; Axel, L.

1989-01-01

To define the lower limits of spatial resolution in gradient-recalled echo phosphorus studies at 1.5 T, the authors have implemented a phosphorus gradient-recalled imaging sequence on the Signa imager. All gradient ramps for the section-selective rephasing lobe, the phase-encoding pulse, and the dephasing pulse of the frequency-encoding gradient are slowed at the maximal rate. Consequently, with a field of view of 24 cm, an in-plane resolution of 3 cm, an echo appropriately offset, an RF bandwidth of 1.2 KHz, and a section thickness of 5 cm, the echo time may be reduced to 1.35 msec. The reconstruction algorithm has been modified to support oversampled data of low spatial resolution appropriate for phosphorus imaging. The sequence will acquire H-1 images and supports the automatic and manual prescan features of the commercial instrument. To facilitate setup in the phosphorus imaging mode the sequence supports the product spectroscopic mode with a DRESS (depth recalled surface coil spectroscopy) sequence and a section profile sequence for appropriate shimming, receiver characteristics, and averaging requirements. The suitability for adaptation of this sequence to three-dimensional chemical shift imaging is discussed

Diffusion-weighted imaging of the rat pelvis using 3D water-excitation MP-RAGE MR sequence

International Nuclear Information System (INIS)

Numano, Tomokazu; Homma, Kazuhiro; Hyodo, Koji; Nitta, Naotaka; Iwasaki, Nobuaki

2008-01-01

We developed a novel technique for fat-saturated, 3-dimensional (3D) diffusion-weighted (DW) magnetic resonance (MR) imaging sequencing based upon the 3D magnetization-prepared, rapid gradient-echo (3D-MP-RAGE) method. We saturated fat using 2 techniques, chemical shift selective (CHESS; FatSat)-3D-DWI sequence versus water excitation (WE)-3D-DWI method, then compared the 2 sequences in terms of degree of fat suppression. In preparing the FatSat-3D-DWI sequence, we used a ''CHESS-90deg radiofrequency (RF)-motion probing gradient (MPG)-180deg RFMPG-90deg RF'' pulse-train, to sensitize the magnetization to fat-saturated diffusion. In contrast, in the WE-3D-DWI sequence, we selected a RAGE-excitation pulse with a binominal-pulse 1-1 or 1-2-1 for water-excited (fat-saturated) diffusion imaging. Experimental results in a phantom confirmed the effects of diffusion weighting and of fat saturation. Fat saturation was much better in the WE-3D-DWI sequence than the CHESS-3D-DWI sequence. From results from animal (rat pelvis) experiments using WE-3D-DWI, we obtained fat-saturated DWI. This sequence was useful for in vivo imaging. (author)

Pulse sequences for contrast-enhanced magnetic resonance imaging

International Nuclear Information System (INIS)

Graves, Martin J.

2007-01-01

The theory and application of magnetic resonance imaging (MRI) pulse sequences following the administration of an exogenous contrast agent are discussed. Pulse sequences are categorised according to the contrast agent mechanism: changes in proton density, relaxivity, magnetic susceptibility and resonant frequency shift. Applications in morphological imaging, magnetic resonance angiography, dynamic imaging and cell labelling are described. The importance of optimising the pulse sequence for each application is emphasised

Post-contrast T1-weighted sequences in pediatric abdominal imaging: comparative analysis of three different sequences and imaging approach

Energy Technology Data Exchange (ETDEWEB)

Roque, Andreia; Ramalho, Miguel; AlObaidy, Mamdoh; Heredia, Vasco; Burke, Lauren M.; De Campos, Rafael O.P.; Semelka, Richard C. [University of North Carolina at Chapel Hill, Department of Radiology, Chapel Hill, NC (United States)

2014-10-15

Post-contrast T1-weighted imaging is an essential component of a comprehensive pediatric abdominopelvic MR examination. However, consistent good image quality is challenging, as respiratory motion in sedated children can substantially degrade the image quality. To compare the image quality of three different post-contrast T1-weighted imaging techniques - standard three-dimensional gradient-echo (3-D-GRE), magnetization-prepared gradient-recall echo (MP-GRE) and 3-D-GRE with radial data sampling (radial 3-D-GRE) - acquired in pediatric patients younger than 5 years of age. Sixty consecutive exams performed in 51 patients (23 females, 28 males; mean age 2.5 ± 1.4 years) constituted the final study population. Thirty-nine scans were performed at 3 T and 21 scans were performed at 1.5 T. Two different reviewers independently and blindly qualitatively evaluated all sequences to determine image quality and extent of artifacts. MP-GRE and radial 3-D-GRE sequences had the least respiratory motion (P < 0.0001). Standard 3-D-GRE sequences displayed the lowest average score ratings in hepatic and pancreatic edge definition, hepatic vessel clarity and overall image quality. Radial 3-D-GRE sequences showed the highest scores ratings in overall image quality. Our preliminary results support the preference of fat-suppressed radial 3-D-GRE as the best post-contrast T1-weighted imaging approach for patients under the age of 5 years, when dynamic imaging is not essential. (orig.)

Rapid-scan EPR imaging.

Science.gov (United States)

Eaton, Sandra S; Shi, Yilin; Woodcock, Lukas; Buchanan, Laura A; McPeak, Joseph; Quine, Richard W; Rinard, George A; Epel, Boris; Halpern, Howard J; Eaton, Gareth R

2017-07-01

In rapid-scan EPR the magnetic field or frequency is repeatedly scanned through the spectrum at rates that are much faster than in conventional continuous wave EPR. The signal is directly-detected with a mixer at the source frequency. Rapid-scan EPR is particularly advantageous when the scan rate through resonance is fast relative to electron spin relaxation rates. In such scans, there may be oscillations on the trailing edge of the spectrum. These oscillations can be removed by mathematical deconvolution to recover the slow-scan absorption spectrum. In cases of inhomogeneous broadening, the oscillations may interfere destructively to the extent that they are not visible. The deconvolution can be used even when it is not required, so spectra can be obtained in which some portions of the spectrum are in the rapid-scan regime and some are not. The technology developed for rapid-scan EPR can be applied generally so long as spectra are obtained in the linear response region. The detection of the full spectrum in each scan, the ability to use higher microwave power without saturation, and the noise filtering inherent in coherent averaging results in substantial improvement in signal-to-noise relative to conventional continuous wave spectroscopy, which is particularly advantageous for low-frequency EPR imaging. This overview describes the principles of rapid-scan EPR and the hardware used to generate the spectra. Examples are provided of its application to imaging of nitroxide radicals, diradicals, and spin-trapped radicals at a Larmor frequency of ca. 250MHz. Copyright © 2017 Elsevier Inc. All rights reserved.

Real-time SPARSE-SENSE cardiac cine MR imaging: optimization of image reconstruction and sequence validation.

Science.gov (United States)

Goebel, Juliane; Nensa, Felix; Bomas, Bettina; Schemuth, Haemi P; Maderwald, Stefan; Gratz, Marcel; Quick, Harald H; Schlosser, Thomas; Nassenstein, Kai

2016-12-01

Improved real-time cardiac magnetic resonance (CMR) sequences have currently been introduced, but so far only limited practical experience exists. This study aimed at image reconstruction optimization and clinical validation of a new highly accelerated real-time cine SPARSE-SENSE sequence. Left ventricular (LV) short-axis stacks of a real-time free-breathing SPARSE-SENSE sequence with high spatiotemporal resolution and of a standard segmented cine SSFP sequence were acquired at 1.5 T in 11 volunteers and 15 patients. To determine the optimal iterations, all volunteers' SPARSE-SENSE images were reconstructed using 10-200 iterations, and contrast ratios, image entropies, and reconstruction times were assessed. Subsequently, the patients' SPARSE-SENSE images were reconstructed with the clinically optimal iterations. LV volumetric values were evaluated and compared between both sequences. Sufficient image quality and acceptable reconstruction times were achieved when using 80 iterations. Bland-Altman plots and Passing-Bablok regression showed good agreement for all volumetric parameters. 80 iterations are recommended for iterative SPARSE-SENSE image reconstruction in clinical routine. Real-time cine SPARSE-SENSE yielded comparable volumetric results as the current standard SSFP sequence. Due to its intrinsic low image acquisition times, real-time cine SPARSE-SENSE imaging with iterative image reconstruction seems to be an attractive alternative for LV function analysis. • A highly accelerated real-time CMR sequence using SPARSE-SENSE was evaluated. • SPARSE-SENSE allows free breathing in real-time cardiac cine imaging. • For clinically optimal SPARSE-SENSE image reconstruction, 80 iterations are recommended. • Real-time SPARSE-SENSE imaging yielded comparable volumetric results as the reference SSFP sequence. • The fast SPARSE-SENSE sequence is an attractive alternative to standard SSFP sequences.

OBJECT-SPACE MULTI-IMAGE MATCHING OF MOBILE-MAPPING-SYSTEM IMAGE SEQUENCES

Directory of Open Access Journals (Sweden)

Y. C. Chen

2012-07-01

Full Text Available This paper proposes an object-space multi-image matching procedure of terrestrial MMS (Mobile Mapping System image sequences to determine the coordinates of an object point automatically and reliably. This image matching procedure can be applied to find conjugate points of MMS image sequences efficiently. Conventional area-based image matching methods are not reliable to deliver accurate matching results for this application due to image scale variations, viewing angle variations, and object occlusions. In order to deal with these three matching problems, an object space multi-image matching is proposed. A modified NCC (Normalized Cross Correlation coefficient is proposed to measure the similarity of image patches. A modified multi-window matching procedure will also be introduced to solve the problem of object occlusion. A coarse-to-fine procedure with a combination of object-space multi-image matching and multi-window matching is adopted. The proposed procedure has been implemented for the purpose of matching terrestrial MMS image sequences. The ratio of correct matches of this experiment was about 80 %. By providing an approximate conjugate point in an overlapping image manually, most of the incorrect matches could be fixed properly and the ratio of correct matches was improved up to 98 %.

Ultra-modified rapid sequence induction with transnasal humidified rapid insufflation ventilatory exchange: Challenging convention

Directory of Open Access Journals (Sweden)

Ketan Sakharam Kulkarni

2018-01-01

Full Text Available During positive pressure ventilation, gastric inflation and subsequent pulmonary aspiration can occur. Rapid sequence induction (RSI technique is an age-old formula to prevent this. We adopted a novel approach of RSI for patients with high risk of aspiration and evaluated it further in patients undergoing laparoscopic surgeries. We believe that, in patients with risk of gastric insufflation and pulmonary aspiration, transnasal humidified rapid-insufflation ventilatory exchange can be useful in facilitating pre- and apnoeic oxygenation till tracheal isolation is achieved.

Pleiades rapid rotators - evidence for an evolutionary sequence

International Nuclear Information System (INIS)

Butler, R.P.; Marcy, G.W.; Cohen, R.D.; Duncan, D.K.; California Univ., La Jolla; Space Telescope Science Institute, Baltimore, MD)

1987-01-01

Four rapidly rotating early-K dwarfs in the Pleiades are shown to contain an order of magnitude more Li than four slow rotators of the same spectral type, as would be expected if they were systematically younger. This supports the idea that late-type stars first arrive on the main sequence with V(rot) greater than about 100 km/s, that they spin down to V(rot) less than about 10 km/s in 10 to the 7th to 10 to the 8th yr, and that the Pleiades lower main sequence shows such an age spread. 14 references

RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data.

Directory of Open Access Journals (Sweden)

Simon H Tausch

Full Text Available The assembly of viral or endosymbiont genomes from Next Generation Sequencing (NGS data is often hampered by the predominant abundance of reads originating from the host organism. These reads increase the memory and CPU time usage of the assembler and can lead to misassemblies.We developed RAMBO-K (Read Assignment Method Based On K-mers, a tool which allows rapid and sensitive removal of unwanted host sequences from NGS datasets. Reaching a speed of 10 Megabases/s on 4 CPU cores and a standard hard drive, RAMBO-K is faster than any tool we tested, while showing a consistently high sensitivity and specificity across different datasets.RAMBO-K rapidly and reliably separates reads from different species without data preprocessing. It is suitable as a straightforward standard solution for workflows dealing with mixed datasets. Binaries and source code (java and python are available from http://sourceforge.net/projects/rambok/.

Image correlation method for DNA sequence alignment.

Science.gov (United States)

Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

2012-01-01

The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

Rapid non-contrast magnetic resonance imaging for post appendectomy intra-abdominal abscess in children

Energy Technology Data Exchange (ETDEWEB)

Lee, Megan H. [Washington University School of Medicine in St. Louis, Mallinckrodt Institute of Radiology, St. Louis, MO (United States); Eutsler, Eric P.; Khanna, Geetika [Washington University School of Medicine in St. Louis, Pediatric Radiology, Mallinckrodt Institute of Radiology, St. Louis, MO (United States); Sheybani, Elizabeth F. [Mercy Hospital St. Louis, Department of Radiology, St. Louis, MO (United States)

2017-07-15

Acute appendicitis, especially if perforated at presentation, is often complicated by postoperative abscess formation. The detection of a postoperative abscess relies primarily on imaging. This has traditionally been done with contrast-enhanced computed tomography. Non-contrast magnetic resonance imaging (MRI) has the potential to accurately detect intra-abdominal abscesses, especially with the use of diffusion-weighted imaging (DWI). To evaluate our single-center experience with a rapid non-contrast MRI protocol evaluating post-appendectomy abscesses in children with persistent postsurgical symptoms. In this retrospective, institutional review board-approved study, all patients underwent a clinically indicated non-contrast 1.5- or 3-Tesla abdomen/pelvis MRI consisting of single-shot fast spin echo, inversion recovery and DWI sequences. All MRI studies were reviewed by two blinded pediatric radiologists to identify the presence of a drainable fluid collection. Each fluid collection was further characterized as accessible or not accessible for percutaneous or transrectal drainage. Imaging findings were compared to clinical outcome. Seven of the 15 patients had a clinically significant fluid collection, and 5 of these patients were treated with percutaneous drain placement or exploratory laparotomy. The other patients had a phlegmon or a clinically insignificant fluid collection and were discharged home within 48 h. Rapid non-contrast MRI utilizing fluid-sensitive and DWI sequences can be used to identify drainable fluid collections in post-appendectomy patients. This protocol can be used to triage patients between conservative management vs. abscess drainage without oral/intravenous contrast or exposure to ionizing radiation. (orig.)

Rapid non-contrast magnetic resonance imaging for post appendectomy intra-abdominal abscess in children

International Nuclear Information System (INIS)

Lee, Megan H.; Eutsler, Eric P.; Khanna, Geetika; Sheybani, Elizabeth F.

2017-01-01

Acute appendicitis, especially if perforated at presentation, is often complicated by postoperative abscess formation. The detection of a postoperative abscess relies primarily on imaging. This has traditionally been done with contrast-enhanced computed tomography. Non-contrast magnetic resonance imaging (MRI) has the potential to accurately detect intra-abdominal abscesses, especially with the use of diffusion-weighted imaging (DWI). To evaluate our single-center experience with a rapid non-contrast MRI protocol evaluating post-appendectomy abscesses in children with persistent postsurgical symptoms. In this retrospective, institutional review board-approved study, all patients underwent a clinically indicated non-contrast 1.5- or 3-Tesla abdomen/pelvis MRI consisting of single-shot fast spin echo, inversion recovery and DWI sequences. All MRI studies were reviewed by two blinded pediatric radiologists to identify the presence of a drainable fluid collection. Each fluid collection was further characterized as accessible or not accessible for percutaneous or transrectal drainage. Imaging findings were compared to clinical outcome. Seven of the 15 patients had a clinically significant fluid collection, and 5 of these patients were treated with percutaneous drain placement or exploratory laparotomy. The other patients had a phlegmon or a clinically insignificant fluid collection and were discharged home within 48 h. Rapid non-contrast MRI utilizing fluid-sensitive and DWI sequences can be used to identify drainable fluid collections in post-appendectomy patients. This protocol can be used to triage patients between conservative management vs. abscess drainage without oral/intravenous contrast or exposure to ionizing radiation. (orig.)

Rapid flow imaging method

International Nuclear Information System (INIS)

Pelc, N.J.; Spritzer, C.E.; Lee, J.N.

1988-01-01

A rapid, phase-contrast, MR imaging method of imaging flow has been implemented. The method, called VIGRE (velocity imaging with gradient recalled echoes), consists of two interleaved, narrow flip angle, gradient-recalled acquisitions. One is flow compensated while the second has a specified flow encoding (both peak velocity and direction) that causes signals to contain additional phase in proportion to velocity in the specified direction. Complex image data from the first acquisition are used as a phase reference for the second, yielding immunity from phase accumulation due to causes other than motion. Images with pixel values equal to MΔΘ where M is the magnitude of the flow compensated image and ΔΘ is the phase difference at the pixel, are produced. The magnitude weighting provides additional vessel contrast, suppresses background noise, maintains the flow direction information, and still allows quantitative data to be retrieved. The method has been validated with phantoms and is undergoing initial clinical evaluation. Early results are extremely encouraging

Visual Perceptual Echo Reflects Learning of Regularities in Rapid Luminance Sequences.

Science.gov (United States)

Chang, Acer Y-C; Schwartzman, David J; VanRullen, Rufin; Kanai, Ryota; Seth, Anil K

2017-08-30

A novel neural signature of active visual processing has recently been described in the form of the "perceptual echo", in which the cross-correlation between a sequence of randomly fluctuating luminance values and occipital electrophysiological signals exhibits a long-lasting periodic (∼100 ms cycle) reverberation of the input stimulus (VanRullen and Macdonald, 2012). As yet, however, the mechanisms underlying the perceptual echo and its function remain unknown. Reasoning that natural visual signals often contain temporally predictable, though nonperiodic features, we hypothesized that the perceptual echo may reflect a periodic process associated with regularity learning. To test this hypothesis, we presented subjects with successive repetitions of a rapid nonperiodic luminance sequence, and examined the effects on the perceptual echo, finding that echo amplitude linearly increased with the number of presentations of a given luminance sequence. These data suggest that the perceptual echo reflects a neural signature of regularity learning.Furthermore, when a set of repeated sequences was followed by a sequence with inverted luminance polarities, the echo amplitude decreased to the same level evoked by a novel stimulus sequence. Crucially, when the original stimulus sequence was re-presented, the echo amplitude returned to a level consistent with the number of presentations of this sequence, indicating that the visual system retained sequence-specific information, for many seconds, even in the presence of intervening visual input. Altogether, our results reveal a previously undiscovered regularity learning mechanism within the human visual system, reflected by the perceptual echo. SIGNIFICANCE STATEMENT How the brain encodes and learns fast-changing but nonperiodic visual input remains unknown, even though such visual input characterizes natural scenes. We investigated whether the phenomenon of "perceptual echo" might index such learning. The perceptual echo is a

Rapid sequence induction and intubation with rocuronium-sugammadex compared with succinylcholine

DEFF Research Database (Denmark)

Sørensen, M K; Bretlau, C; Gätke, M R

2012-01-01

An unanticipated difficult airway may arise during rapid sequence induction and intubation (RSII). The aim of the trial was to assess how rapidly spontaneous ventilation could be re-established after RSII. We hypothesized that the time period from tracheal intubation to spontaneous ventilation wo...... would be shorter with rocuronium-sugammadex than with succinylcholine....

Age-Related Declines in Early Sensory Memory: Identification of Rapid Auditory and Visual Stimulus Sequences.

Science.gov (United States)

Fogerty, Daniel; Humes, Larry E; Busey, Thomas A

2016-01-01

Age-related temporal-processing declines of rapidly presented sequences may involve contributions of sensory memory. This study investigated recall for rapidly presented auditory (vowel) and visual (letter) sequences presented at six different stimulus onset asynchronies (SOA) that spanned threshold SOAs for sequence identification. Younger, middle-aged, and older adults participated in all tasks. Results were investigated at both equivalent performance levels (i.e., SOA threshold) and at identical physical stimulus values (i.e., SOAs). For four-item sequences, results demonstrated best performance for the first and last items in the auditory sequences, but only the first item for visual sequences. For two-item sequences, adults identified the second vowel or letter significantly better than the first. Overall, when temporal-order performance was equated for each individual by testing at SOA thresholds, recall accuracy for each position across the age groups was highly similar. These results suggest that modality-specific processing declines of older adults primarily determine temporal-order performance for rapid sequences. However, there is some evidence for a second amodal processing decline in older adults related to early sensory memory for final items in a sequence. This selective deficit was observed particularly for longer sequence lengths and was not accounted for by temporal masking.

Image ranking in video sequences using pairwise image comparisons and temporal smoothing

CSIR Research Space (South Africa)

Burke, Michael

2016-12-01

Full Text Available The ability to predict the importance of an image is highly desirable in computer vision. This work introduces an image ranking scheme suitable for use in video or image sequences. Pairwise image comparisons are used to determine image ‘interest...

Rapid MRI evaluation of acute intracranial hemorrhage in pediatric head trauma

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Ryan, Maura E.; Jaju, Alok [Northwestern University Feinberg School of Medicine, Department of Radiology, Chicago, IL (United States); Ann and Robert H. Lurie Children' s Hospital of Chicago, Department of Medical Imaging, Chicago, IL (United States); Ciolino, Jody D. [Northwestern University, Biostatistics Collaboration Center, Department of Preventive Medicine Feinberg School of Medicine, Chicago, IL (United States); Alden, Tord [Northwestern University Feinberg School of Medicine, Department of Neurological Surgery, Chicago, IL (United States); Ann and Robert H. Lurie Children' s Hospital of Chicago, Department of Neurosurgery, Chicago, IL (United States)

2016-08-15

Rapid MRI with ultrafast T2 sequences can be performed without sedation and is often used in place of computed tomography (CT) to evaluate pediatric patients for indications such as hydrocephalus. This study investigated the sensitivity of rapid magnetic resonance imaging (MRI) for detection and follow-up of acute intracranial hemorrhage in comparison to CT, which is commonly the first-line imaging. Patients presenting to a pediatric hospital with acute intracranial hemorrhage on CT and follow-up rapid MRI within 48 h were included. Rapid MRI studies consisted of three plane ultrafast T2 sequences either with or without axial gradient echo (GRE) sequences. Identification of hemorrhage on rapid MRI was assessed by readers both blinded and unblinded to prior CT results. One hundred two acute hemorrhages in 61 patients were identified by CT. Rapid MRI detection of subdural and epidural hemorrhages was modest in the absence of prior CT for comparison (sensitivity 61-74 %), but increased with review of the prior CT (sensitivity 80-86 %). Hemorrhage size was a significant predictor of detection (p < 0.0001). Three plane fast T2 images alone without GRE sequences were poor at detecting subarachnoid hemorrhage (sensitivity 10-25 %); rapid MRI with GRE sequences identified the majority of subarachnoid hemorrhage (sensitivity 71-93 %). GRE modestly increased detection of other extra-axial hemorrhages. Rapid MRI with GRE sequences is sensitive for most acute intracranial hemorrhages only when a prior CT is available for review. Rapid MRI is not adequate to replace CT in initial evaluation of intracranial hemorrhages but may be helpful in follow-up of known hemorrhages. (orig.)

Rapid MRI evaluation of acute intracranial hemorrhage in pediatric head trauma

International Nuclear Information System (INIS)

Ryan, Maura E.; Jaju, Alok; Ciolino, Jody D.; Alden, Tord

2016-01-01

Rapid MRI with ultrafast T2 sequences can be performed without sedation and is often used in place of computed tomography (CT) to evaluate pediatric patients for indications such as hydrocephalus. This study investigated the sensitivity of rapid magnetic resonance imaging (MRI) for detection and follow-up of acute intracranial hemorrhage in comparison to CT, which is commonly the first-line imaging. Patients presenting to a pediatric hospital with acute intracranial hemorrhage on CT and follow-up rapid MRI within 48 h were included. Rapid MRI studies consisted of three plane ultrafast T2 sequences either with or without axial gradient echo (GRE) sequences. Identification of hemorrhage on rapid MRI was assessed by readers both blinded and unblinded to prior CT results. One hundred two acute hemorrhages in 61 patients were identified by CT. Rapid MRI detection of subdural and epidural hemorrhages was modest in the absence of prior CT for comparison (sensitivity 61-74 %), but increased with review of the prior CT (sensitivity 80-86 %). Hemorrhage size was a significant predictor of detection (p < 0.0001). Three plane fast T2 images alone without GRE sequences were poor at detecting subarachnoid hemorrhage (sensitivity 10-25 %); rapid MRI with GRE sequences identified the majority of subarachnoid hemorrhage (sensitivity 71-93 %). GRE modestly increased detection of other extra-axial hemorrhages. Rapid MRI with GRE sequences is sensitive for most acute intracranial hemorrhages only when a prior CT is available for review. Rapid MRI is not adequate to replace CT in initial evaluation of intracranial hemorrhages but may be helpful in follow-up of known hemorrhages. (orig.)

A New Images Hiding Scheme Based on Chaotic Sequences

Institute of Scientific and Technical Information of China (English)

LIU Nian-sheng; GUO Dong-hui; WU Bo-xi; Parr G

2005-01-01

We propose a data hidding technique in a still image. This technique is based on chaotic sequence in the transform domain of covert image. We use different chaotic random sequences multiplied by multiple sensitive images, respectively, to spread the spectrum of sensitive images. Multiple sensitive images are hidden in a covert image as a form of noise. The results of theoretical analysis and computer simulation show the new hiding technique have better properties with high security, imperceptibility and capacity for hidden information in comparison with the conventional scheme such as LSB (Least Significance Bit).

Statistical processing of large image sequences.

Science.gov (United States)

Khellah, F; Fieguth, P; Murray, M J; Allen, M

2005-01-01

The dynamic estimation of large-scale stochastic image sequences, as frequently encountered in remote sensing, is important in a variety of scientific applications. However, the size of such images makes conventional dynamic estimation methods, for example, the Kalman and related filters, impractical. In this paper, we present an approach that emulates the Kalman filter, but with considerably reduced computational and storage requirements. Our approach is illustrated in the context of a 512 x 512 image sequence of ocean surface temperature. The static estimation step, the primary contribution here, uses a mixture of stationary models to accurately mimic the effect of a nonstationary prior, simplifying both computational complexity and modeling. Our approach provides an efficient, stable, positive-definite model which is consistent with the given correlation structure. Thus, the methods of this paper may find application in modeling and single-frame estimation.

Digital image sequence processing, compression, and analysis

CERN Document Server

Reed, Todd R

2004-01-01

IntroductionTodd R. ReedCONTENT-BASED IMAGE SEQUENCE REPRESENTATIONPedro M. Q. Aguiar, Radu S. Jasinschi, José M. F. Moura, andCharnchai PluempitiwiriyawejTHE COMPUTATION OF MOTIONChristoph Stiller, Sören Kammel, Jan Horn, and Thao DangMOTION ANALYSIS AND DISPLACEMENT ESTIMATION IN THE FREQUENCY DOMAINLuca Lucchese and Guido Maria CortelazzoQUALITY OF SERVICE ASSESSMENT IN NEW GENERATION WIRELESS VIDEO COMMUNICATIONSGaetano GiuntaERROR CONCEALMENT IN DIGITAL VIDEOFrancesco G.B. De NataleIMAGE SEQUENCE RESTORATION: A WIDER PERSPECTIVEAnil KokaramVIDEO SUMMARIZATIONCuneyt M. Taskiran and Edward

Fat suppression in MR imaging with binomial pulse sequences

International Nuclear Information System (INIS)

Baudovin, C.J.; Bryant, D.J.; Bydder, G.M.; Young, I.R.

1989-01-01

This paper reports on a study to develop pulse sequences allowing suppression of fat signal on MR images without eliminating signal from other tissues with short T1. They have developed such a technique involving selective excitation of protons in water, based on a binomial pulse sequence. Imaging is performed at 0.15 T. Careful shimming is performed to maximize separation of fat and water peaks. A spin-echo 1,500/80 sequence is used, employing 90 degrees pulse with transit frequency optimized for water with null excitation of 20 H offset, followed by a section-selective 180 degrees pulse. With use of the binomial sequence for imagining, reduction in fat signal is seen on images of the pelvis and legs of volunteers. Patient studies show dramatic improvement in visualization of prostatic carcinoma compared with standard sequences

MR imaging pulse sequence rationale: SD-, T1-, and T2-weighted images

International Nuclear Information System (INIS)

Sax, S.; Weathers, S.W.; Schneiders, N.J.; Horowitz, B.L.; Mawad, M.E.; Sandlin, M.E.; Blackwell, R.; Bryan, R.N.

1986-01-01

Over 500 patients have been examined with a pulse sequence designed to provide spin-density (SD)-weighted images (TR=3 sec, TE=35 msec), T1-weighted images (TR=0.3 sec, TE=35msec), and T2-weighted images (TR=3 sec, TE=105 msec) from which calculated ''synthesized'' images and SD, T1, and T2 calculated images could be obtained. Each image contributes unique information. SD-weighted images optimally display anatomy and often best highlight pathology. T1-weighted images are critical in assessing cerebral hemorrhages. T2-weighted images best display most lesions, but yield incomplete information in 35% of cases. All three types of ''weighted'' images are necessary to optimally display anatomy and fully characterize a lesion. Computerized calculations and simulations suggest that no other combination of pulse sequences yields equal information for a given examination time

Motion Detection in Ultrasound Image-Sequences Using Tensor Voting

Science.gov (United States)

Inba, Masafumi; Yanagida, Hirotaka; Tamura, Yasutaka

2008-05-01

Motion detection in ultrasound image sequences using tensor voting is described. We have been developing an ultrasound imaging system adopting a combination of coded excitation and synthetic aperture focusing techniques. In our method, frame rate of the system at distance of 150 mm reaches 5000 frame/s. Sparse array and short duration coded ultrasound signals are used for high-speed data acquisition. However, many artifacts appear in the reconstructed image sequences because of the incompleteness of the transmitted code. To reduce the artifacts, we have examined the application of tensor voting to the imaging method which adopts both coded excitation and synthetic aperture techniques. In this study, the basis of applying tensor voting and the motion detection method to ultrasound images is derived. It was confirmed that velocity detection and feature enhancement are possible using tensor voting in the time and space of simulated ultrasound three-dimensional image sequences.

Image sequence analysis workstation for multipoint motion analysis

Science.gov (United States)

Mostafavi, Hassan

1990-08-01

This paper describes an application-specific engineering workstation designed and developed to analyze motion of objects from video sequences. The system combines the software and hardware environment of a modem graphic-oriented workstation with the digital image acquisition, processing and display techniques. In addition to automation and Increase In throughput of data reduction tasks, the objective of the system Is to provide less invasive methods of measurement by offering the ability to track objects that are more complex than reflective markers. Grey level Image processing and spatial/temporal adaptation of the processing parameters is used for location and tracking of more complex features of objects under uncontrolled lighting and background conditions. The applications of such an automated and noninvasive measurement tool include analysis of the trajectory and attitude of rigid bodies such as human limbs, robots, aircraft in flight, etc. The system's key features are: 1) Acquisition and storage of Image sequences by digitizing and storing real-time video; 2) computer-controlled movie loop playback, freeze frame display, and digital Image enhancement; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored Image sequence; 4) model-based estimation and tracking of the six degrees of freedom of a rigid body: 5) field-of-view and spatial calibration: 6) Image sequence and measurement data base management; and 7) offline analysis software for trajectory plotting and statistical analysis.

Centrifuge: rapid and sensitive classification of metagenomic sequences.

Science.gov (United States)

Kim, Daehwan; Song, Li; Breitwieser, Florian P; Salzberg, Steven L

2016-12-01

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space. © 2016 Kim et al.; Published by Cold Spring Harbor Laboratory Press.

Fast high-resolution MR imaging using the snapshot-FLASH MR sequence

International Nuclear Information System (INIS)

Matthaei, D.; Haase, A.; Henrich, D.; Duhmke, E.

1990-01-01

Snapshot, fast low-angle short (FLASH) MR imaging using an accelerated FLASH-MR sequence provides MR images with measuring times far below 1 second. The short TE of this sequence prevents susceptibility artifacts in gradient-echo imaging. In this paper variations of the sequence are shown that provide high resolution images with T1-weighted IR, T2-weighted SE, and chemical shift (CHESS) contrast sequences. METHODS AND MATERIALS: A whole-body 2-T system (Bruker-Medizintechnik) were used in combination with a 60-cm gradient system (providing gradient strength of 5 mT/m) to study healthy volunteers. The measuring time for a 256 x 256 image matrix was 800 msec. This sequence has been used in combination with T1-weighted IR, T2-weighted SE, and CHESS variations

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

Science.gov (United States)

Wala, Jeremiah; Beroukhim, Rameen

2017-03-01

We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Temporal characteristics of radiologists’ and novices’ lesion detection in viewing medical images presented rapidly and sequentially

Directory of Open Access Journals (Sweden)

Ryoichi Nakashima

2016-10-01

Full Text Available Although viewing multiple stacks of medical images presented on a display is a relatively new but useful medical task, little is known about this task. Particularly, it is unclear how radiologists search for lesions in this type of image reading. When viewing cluttered and dynamic displays, continuous motion itself does not capture attention. Thus, it is effective for the target detection that observers’ attention is captured by the onset signal of a suddenly appearing target among the continuously moving distractors (i.e., a passive viewing strategy. This can be applied to stack viewing tasks, because lesions often show up as transient signals in medical images which are sequentially presented simulating a dynamic and smoothly transforming image progression of organs. However, it is unclear whether observers can detect a target when the target appears at the beginning of a sequential presentation where the global apparent motion onset signal (i.e., signal of the initiation of the apparent motion by sequential presentation occurs. We investigated the ability of radiologists to detect lesions during such tasks by comparing the performances of radiologists and novices. Results show that overall performance of radiologists is better than novices. Furthermore, the temporal locations of lesions in CT image sequences, i.e., when a lesion appears in an image sequence, does not affect the performance of radiologists, whereas it does affect the performance of novices. Results indicate that novices have greater difficulty in detecting a lesion appearing early than late in the image sequence. We suggest that radiologists have other mechanisms to detect lesions in medical images with little attention which novices do not have. This ability is critically important when viewing rapid sequential presentations of multiple CT images, such as stack viewing tasks.

Rapid analysis and exploration of fluorescence microscopy images.

Science.gov (United States)

Pavie, Benjamin; Rajaram, Satwik; Ouyang, Austin; Altschuler, Jason M; Steininger, Robert J; Wu, Lani F; Altschuler, Steven J

2014-03-19

Despite rapid advances in high-throughput microscopy, quantitative image-based assays still pose significant challenges. While a variety of specialized image analysis tools are available, most traditional image-analysis-based workflows have steep learning curves (for fine tuning of analysis parameters) and result in long turnaround times between imaging and analysis. In particular, cell segmentation, the process of identifying individual cells in an image, is a major bottleneck in this regard. Here we present an alternate, cell-segmentation-free workflow based on PhenoRipper, an open-source software platform designed for the rapid analysis and exploration of microscopy images. The pipeline presented here is optimized for immunofluorescence microscopy images of cell cultures and requires minimal user intervention. Within half an hour, PhenoRipper can analyze data from a typical 96-well experiment and generate image profiles. Users can then visually explore their data, perform quality control on their experiment, ensure response to perturbations and check reproducibility of replicates. This facilitates a rapid feedback cycle between analysis and experiment, which is crucial during assay optimization. This protocol is useful not just as a first pass analysis for quality control, but also may be used as an end-to-end solution, especially for screening. The workflow described here scales to large data sets such as those generated by high-throughput screens, and has been shown to group experimental conditions by phenotype accurately over a wide range of biological systems. The PhenoBrowser interface provides an intuitive framework to explore the phenotypic space and relate image properties to biological annotations. Taken together, the protocol described here will lower the barriers to adopting quantitative analysis of image based screens.

On the Usage of GPUs for Efficient Motion Estimation in Medical Image Sequences

Directory of Open Access Journals (Sweden)

Jeyarajan Thiyagalingam

2011-01-01

Full Text Available Images are ubiquitous in biomedical applications from basic research to clinical practice. With the rapid increase in resolution, dimensionality of the images and the need for real-time performance in many applications, computational requirements demand proper exploitation of multicore architectures. Towards this, GPU-specific implementations of image analysis algorithms are particularly promising. In this paper, we investigate the mapping of an enhanced motion estimation algorithm to novel GPU-specific architectures, the resulting challenges and benefits therein. Using a database of three-dimensional image sequences, we show that the mapping leads to substantial performance gains, up to a factor of 60, and can provide near-real-time experience. We also show how architectural peculiarities of these devices can be best exploited in the benefit of algorithms, most specifically for addressing the challenges related to their access patterns and different memory configurations. Finally, we evaluate the performance of the algorithm on three different GPU architectures and perform a comprehensive analysis of the results.

Quantitative comparison between a multiecho sequence and a single-echo sequence for susceptibility-weighted phase imaging.

Science.gov (United States)

Gilbert, Guillaume; Savard, Geneviève; Bard, Céline; Beaudoin, Gilles

2012-06-01

The aim of this study was to investigate the benefits arising from the use of a multiecho sequence for susceptibility-weighted phase imaging using a quantitative comparison with a standard single-echo acquisition. Four healthy adult volunteers were imaged on a clinical 3-T system using a protocol comprising two different three-dimensional susceptibility-weighted gradient-echo sequences: a standard single-echo sequence and a multiecho sequence. Both sequences were repeated twice in order to evaluate the local noise contribution by a subtraction of the two acquisitions. For the multiecho sequence, the phase information from each echo was independently unwrapped, and the background field contribution was removed using either homodyne filtering or the projection onto dipole fields method. The phase information from all echoes was then combined using a weighted linear regression. R2 maps were also calculated from the multiecho acquisitions. The noise standard deviation in the reconstructed phase images was evaluated for six manually segmented regions of interest (frontal white matter, posterior white matter, globus pallidus, putamen, caudate nucleus and lateral ventricle). The use of the multiecho sequence for susceptibility-weighted phase imaging led to a reduction of the noise standard deviation for all subjects and all regions of interest investigated in comparison to the reference single-echo acquisition. On average, the noise reduction ranged from 18.4% for the globus pallidus to 47.9% for the lateral ventricle. In addition, the amount of noise reduction was found to be strongly inversely correlated to the estimated R2 value (R=-0.92). In conclusion, the use of a multiecho sequence is an effective way to decrease the noise contribution in susceptibility-weighted phase images, while preserving both contrast and acquisition time. The proposed approach additionally permits the calculation of R2 maps. Copyright © 2012 Elsevier Inc. All rights reserved.

Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

KAUST Repository

Coll, Francesc

2015-05-27

Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.

Rapid Analysis and Exploration of Fluorescence Microscopy Images

OpenAIRE

Pavie, Benjamin; Rajaram, Satwik; Ouyang, Austin; Altschuler, Jason; Steininger, Robert J; Wu, Lani; Altschuler, Steven

2014-01-01

Despite rapid advances in high-throughput microscopy, quantitative image-based assays still pose significant challenges. While a variety of specialized image analysis tools are available, most traditional image-analysis-based workflows have steep learning curves (for fine tuning of analysis parameters) and result in long turnaround times between imaging and analysis. In particular, cell segmentation, the process of identifying individual cells in an image, is a major bottleneck in this regard.

Fast T1-weighted imaging using GRASE sequence for the female pelvis

International Nuclear Information System (INIS)

Dohke, Masako; Watanabe, Yuji; Kumashiro, Masayuki; Amoh, Yoshiki; Ishimori, Takayoshi; Oda, Kazushige; Okumura, Akira; Koike, Shinji; Dodo, Yoshihiro

1998-01-01

GRASE sequence, a combination of TSE and gradient echo, has been developed as a fast T 2 -weighted imaging technique. We have modified the GRASE sequence to be used for fast T 1 -weighted imaging of the female pelvis. In this article, we compared image quality and incidence of artifacts between T 1 -weighted GRASE images and conventional T 1 -weighted SE images. In a phantom study, signal-to-noise ratio was inferior in the GRASE images relative to corresponding on SE images. Susceptibility and chemical shift artifacts seen in GRASE images were seen with almost equal incidence in SE and TSE images. In a clinical study, we compared GRASE images with SE images in six patients with endometrial cysts and four patients with dermoid cysts. The overall image quality obtained with GRASE sequence was satisfactory in all patients and was almost identical with that obtained with SE sequence. GRASE images demonstrated endometrial cysts and dermoid cysts as clearly as did SE images. T 1 -weighted GRASE imaging, however, has a relatively long TE (35 ms) for T 1 -weighted images, which makes the signal intensity of urine and uterine endometrium with long T 2 values higher than in SE images. In conclusion, GRASE sequence can be used for fast T 1 -weighted imaging of the female pelvis because of short imaging time. (author)

Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines.

Science.gov (United States)

Oliveira, Francisco P M; Tavares, João Manuel R S

2013-03-01

This article presents an enhanced methodology to align plantar pressure image sequences simultaneously in time and space. The temporal alignment of the sequences is accomplished using B-splines in the time modeling, and the spatial alignment can be attained using several geometric transformation models. The methodology was tested on a dataset of 156 real plantar pressure image sequences (3 sequences for each foot of the 26 subjects) that was acquired using a common commercial plate during barefoot walking. In the alignment of image sequences that were synthetically deformed both in time and space, an outstanding accuracy was achieved with the cubic B-splines. This accuracy was significantly better (p align real image sequences with unknown transformation involved, the alignment based on cubic B-splines also achieved superior results than our previous methodology (p alignment on the dynamic center of pressure (COP) displacement was also assessed by computing the intraclass correlation coefficients (ICC) before and after the temporal alignment of the three image sequence trials of each foot of the associated subject at six time instants. The results showed that, generally, the ICCs related to the medio-lateral COP displacement were greater when the sequences were temporally aligned than the ICCs of the original sequences. Based on the experimental findings, one can conclude that the cubic B-splines are a remarkable solution for the temporal alignment of plantar pressure image sequences. These findings also show that the temporal alignment can increase the consistency of the COP displacement on related acquired plantar pressure image sequences.

Functional brain activation differences in stuttering identified with a rapid fMRI sequence

Science.gov (United States)

Kraft, Shelly Jo; Choo, Ai Leen; Sharma, Harish; Ambrose, Nicoline G.

2011-01-01

The purpose of this study was to investigate whether brain activity related to the presence of stuttering can be identified with rapid functional MRI (fMRI) sequences that involved overt and covert speech processing tasks. The long-term goal is to develop sensitive fMRI approaches with developmentally appropriate tasks to identify deviant speech motor and auditory brain activity in children who stutter closer to the age at which recovery from stuttering is documented. Rapid sequences may be preferred for individuals or populations who do not tolerate long scanning sessions. In this report, we document the application of a picture naming and phoneme monitoring task in three minute fMRI sequences with adults who stutter (AWS). If relevant brain differences are found in AWS with these approaches that conform to previous reports, then these approaches can be extended to younger populations. Pairwise contrasts of brain BOLD activity between AWS and normally fluent adults indicated the AWS showed higher BOLD activity in the right inferior frontal gyrus (IFG), right temporal lobe and sensorimotor cortices during picture naming and and higher activity in the right IFG during phoneme monitoring. The right lateralized pattern of BOLD activity together with higher activity in sensorimotor cortices is consistent with previous reports, which indicates rapid fMRI sequences can be considered for investigating stuttering in younger participants. PMID:22133409

CT Image Sequence Restoration Based on Sparse and Low-Rank Decomposition

Science.gov (United States)

Gou, Shuiping; Wang, Yueyue; Wang, Zhilong; Peng, Yong; Zhang, Xiaopeng; Jiao, Licheng; Wu, Jianshe

2013-01-01

Blurry organ boundaries and soft tissue structures present a major challenge in biomedical image restoration. In this paper, we propose a low-rank decomposition-based method for computed tomography (CT) image sequence restoration, where the CT image sequence is decomposed into a sparse component and a low-rank component. A new point spread function of Weiner filter is employed to efficiently remove blur in the sparse component; a wiener filtering with the Gaussian PSF is used to recover the average image of the low-rank component. And then we get the recovered CT image sequence by combining the recovery low-rank image with all recovery sparse image sequence. Our method achieves restoration results with higher contrast, sharper organ boundaries and richer soft tissue structure information, compared with existing CT image restoration methods. The robustness of our method was assessed with numerical experiments using three different low-rank models: Robust Principle Component Analysis (RPCA), Linearized Alternating Direction Method with Adaptive Penalty (LADMAP) and Go Decomposition (GoDec). Experimental results demonstrated that the RPCA model was the most suitable for the small noise CT images whereas the GoDec model was the best for the large noisy CT images. PMID:24023764

New diffusion imaging method with a single acquisition sequence

International Nuclear Information System (INIS)

Melki, Ph.S.; Bittoun, J.; Lefevre, J.E.

1987-01-01

The apparent diffusion coefficient (ADC) is related to the molecular diffusion coefficient and to physiologic information: microcirculation in the capillary network, incoherent slow flow, and restricted diffusion. The authors present a new MR imaging sequence that yields computed ADC images in only one acquisition of 9-minutes with a 1.5-T imager (GE Signa). Compared to the previous method, this sequence is at least two times faster and thus can be used as a routine examination to supplement T1-, T2-, and density-weighted images. The method was assessed by measurement of the molecular diffusion in liquids, and the first clinical images obtained in neurologic diseases demonstrate its efficiency for clinical investigation. The possibility of separately imaging diffusion and perfusion is supported by an algorithm

Rapid detection of SMARCB1 sequence variation using high resolution melting

Directory of Open Access Journals (Sweden)

Ashley David M

2009-12-01

Full Text Available Abstract Background Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM, for detecting sequence variations in SMARCB1. Methods Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. Results The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4% showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA. A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. Conclusions This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to

Rapid detection of SMARCB1 sequence variation using high resolution melting

International Nuclear Information System (INIS)

Dagar, Vinod; Chow, Chung-Wo; Ashley, David M; Algar, Elizabeth M

2009-01-01

Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening

Effectiveness of a Rapid Lumbar Spine MRI Protocol Using 3D T2-Weighted SPACE Imaging Versus a Standard Protocol for Evaluation of Degenerative Changes of the Lumbar Spine.

Science.gov (United States)

Sayah, Anousheh; Jay, Ann K; Toaff, Jacob S; Makariou, Erini V; Berkowitz, Frank

2016-09-01

Reducing lumbar spine MRI scanning time while retaining diagnostic accuracy can benefit patients and reduce health care costs. This study compares the effectiveness of a rapid lumbar MRI protocol using 3D T2-weighted sampling perfection with application-optimized contrast with different flip-angle evolutions (SPACE) sequences with a standard MRI protocol for evaluation of lumbar spondylosis. Two hundred fifty consecutive unenhanced lumbar MRI examinations performed at 1.5 T were retrospectively reviewed. Full, rapid, and complete versions of each examination were interpreted for spondylotic changes at each lumbar level, including herniations and neural compromise. The full examination consisted of sagittal T1-weighted, T2-weighted turbo spin-echo (TSE), and STIR sequences; and axial T1- and T2-weighted TSE sequences (time, 18 minutes 40 seconds). The rapid examination consisted of sagittal T1- and T2-weighted SPACE sequences, with axial SPACE reformations (time, 8 minutes 46 seconds). The complete examination consisted of the full examination plus the T2-weighted SPACE sequence. Sensitivities and specificities of the full and rapid examinations were calculated using the complete study as the reference standard. The rapid and full studies had sensitivities of 76.0% and 69.3%, with specificities of 97.2% and 97.9%, respectively, for all degenerative processes. Rapid and full sensitivities were 68.7% and 66.3% for disk herniation, 85.2% and 81.5% for canal compromise, 82.9% and 69.1% for lateral recess compromise, and 76.9% and 69.7% for foraminal compromise, respectively. Isotropic SPACE T2-weighted imaging provides high-quality imaging of lumbar spondylosis, with multiplanar reformatting capability. Our SPACE-based rapid protocol had sensitivities and specificities for herniations and neural compromise comparable to those of the protocol without SPACE. This protocol fits within a 15-minute slot, potentially reducing costs and discomfort for a large subgroup of

Investigating the feasibility of rapid MRI for image-guided motion management in lung cancer radiotherapy.

Science.gov (United States)

Sawant, Amit; Keall, Paul; Pauly, Kim Butts; Alley, Marcus; Vasanawala, Shreyas; Loo, Billy W; Hinkle, Jacob; Joshi, Sarang

2014-01-01

Cycle-to-cycle variations in respiratory motion can cause significant geometric and dosimetric errors in the administration of lung cancer radiation therapy. A common limitation of the current strategies for motion management is that they assume a constant, reproducible respiratory cycle. In this work, we investigate the feasibility of using rapid MRI for providing long-term imaging of the thorax in order to better capture cycle-to-cycle variations. Two nonsmall-cell lung cancer patients were imaged (free-breathing, no extrinsic contrast, and 1.5 T scanner). A balanced steady-state-free-precession (b-SSFP) sequence was used to acquire cine-2D and cine-3D (4D) images. In the case of Patient 1 (right midlobe lesion, ~40 mm diameter), tumor motion was well correlated with diaphragmatic motion. In the case of Patient 2, (left upper-lobe lesion, ~60 mm diameter), tumor motion was poorly correlated with diaphragmatic motion. Furthermore, the motion of the tumor centroid was poorly correlated with the motion of individual points on the tumor boundary, indicating significant rotation and/or deformation. These studies indicate that image quality and acquisition speed of cine-2D MRI were adequate for motion monitoring. However, significant improvements are required to achieve comparable speeds for truly 4D MRI. Despite several challenges, rapid MRI offers a feasible and attractive tool for noninvasive, long-term motion monitoring.

Denoising time-resolved microscopy image sequences with singular value thresholding

Energy Technology Data Exchange (ETDEWEB)

Furnival, Tom, E-mail: tjof2@cam.ac.uk; Leary, Rowan K., E-mail: rkl26@cam.ac.uk; Midgley, Paul A., E-mail: pam33@cam.ac.uk

2017-07-15

Time-resolved imaging in microscopy is important for the direct observation of a range of dynamic processes in both the physical and life sciences. However, the image sequences are often corrupted by noise, either as a result of high frame rates or a need to limit the radiation dose received by the sample. Here we exploit both spatial and temporal correlations using low-rank matrix recovery methods to denoise microscopy image sequences. We also make use of an unbiased risk estimator to address the issue of how much thresholding to apply in a robust and automated manner. The performance of the technique is demonstrated using simulated image sequences, as well as experimental scanning transmission electron microscopy data, where surface adatom motion and nanoparticle structural dynamics are recovered at rates of up to 32 frames per second. - Highlights: • Correlations in space and time are harnessed to denoise microscopy image sequences. • A robust estimator provides automated selection of the denoising parameter. • Motion tracking and automated noise estimation provides a versatile algorithm. • Application to time-resolved STEM enables study of atomic and nanoparticle dynamics.

Rapid resistome mapping using nanopore sequencing.

Science.gov (United States)

van der Helm, Eric; Imamovic, Lejla; Hashim Ellabaan, Mostafa M; van Schaik, Willem; Koza, Anna; Sommer, Morten O A

2017-05-05

The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine. The outcome of antibiotic treatment can be affected by the composition of the gut. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU (intensive care unit) patient. The accuracy of the poreFUME pipeline is with >97% sufficient for the annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Image encryption using random sequence generated from generalized information domain

International Nuclear Information System (INIS)

Zhang Xia-Yan; Wu Jie-Hua; Zhang Guo-Ji; Li Xuan; Ren Ya-Zhou

2016-01-01

A novel image encryption method based on the random sequence generated from the generalized information domain and permutation–diffusion architecture is proposed. The random sequence is generated by reconstruction from the generalized information file and discrete trajectory extraction from the data stream. The trajectory address sequence is used to generate a P-box to shuffle the plain image while random sequences are treated as keystreams. A new factor called drift factor is employed to accelerate and enhance the performance of the random sequence generator. An initial value is introduced to make the encryption method an approximately one-time pad. Experimental results show that the random sequences pass the NIST statistical test with a high ratio and extensive analysis demonstrates that the new encryption scheme has superior security. (paper)

A rapid compression technique for 4-D functional MRI images using data rearrangement and modified binary array techniques.

Science.gov (United States)

Uma Vetri Selvi, G; Nadarajan, R

2015-12-01

Compression techniques are vital for efficient storage and fast transfer of medical image data. The existing compression techniques take significant amount of time for performing encoding and decoding and hence the purpose of compression is not fully satisfied. In this paper a rapid 4-D lossy compression method constructed using data rearrangement, wavelet-based contourlet transformation and a modified binary array technique has been proposed for functional magnetic resonance imaging (fMRI) images. In the proposed method, the image slices of fMRI data are rearranged so that the redundant slices form a sequence. The image sequence is then divided into slices and transformed using wavelet-based contourlet transform (WBCT). In WBCT, the high frequency sub-band obtained from wavelet transform is further decomposed into multiple directional sub-bands by directional filter bank to obtain more directional information. The relationship between the coefficients has been changed in WBCT as it has more directions. The differences in parent–child relationships are handled by a repositioning algorithm. The repositioned coefficients are then subjected to quantization. The quantized coefficients are further compressed by modified binary array technique where the most frequently occurring value of a sequence is coded only once. The proposed method has been experimented with fMRI images the results indicated that the processing time of the proposed method is less compared to existing wavelet-based set partitioning in hierarchical trees and set partitioning embedded block coder (SPECK) compression schemes [1]. The proposed method could also yield a better compression performance compared to wavelet-based SPECK coder. The objective results showed that the proposed method could gain good compression ratio in maintaining a peak signal noise ratio value of above 70 for all the experimented sequences. The SSIM value is equal to 1 and the value of CC is greater than 0.9 for all

MR imaging of articular cartilage in the ankle: comparison of available imaging sequences and methods of measurement in cadavers

Energy Technology Data Exchange (ETDEWEB)

Tan, T.C.F. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States)]|[Department of Radiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan (Taiwan, Province of China); Wilcox, D.M. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States); Frank, L. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States); Shih, C. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States)]|[Department of Radiology, Veterans General Hospital-Taipei (Taiwan, Province of China); Trudell, D.J. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States); Sartoris, D.J. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States); Resnick, D. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States)

1996-11-01

Objective. To assess hyaline cartilage of cadaveric ankles using different magnetic resonance (MR) imaging techniques and various methods of measurement. Design and patients. Cartilage thicknesses of the talus and tibia were measured in ten cadaveric ankles by naked eye and by digitized image analysis from MR images of fat-suppressed T1-weighted gradient recalled (FS-SPGR), sequences and pulsed transfer saturation sequences with (FS-STS) and without fat-suppression (STS); these measurements were compared with those derived from direct inspection of cadaveric sections. The accuracy and precision errors were evaluated statistically for each imaging technique as well as measuring method. Contrast-to-noise ratios of cartilage versus joint fluid and marrow were compared for each of the imaging sequences. Results. Statistically, measurements from FS-SPGR images were associated with the smallest estimation error. Precision error of measurements derived from digitized image analysis was found to be smaller than that derived from naked eye measurements. Cartilage thickness measurements in images from STS and FS-STS sequences revealed larger errors in both accuracy and precision. Interobserver variance was larger in naked eye assessment of the cartilage. Contrast-to-noise ratio of cartilage versus joint fluid and marrow was higher with FS-SPGR than with FS-STS or STS sequences. Conclusion. Of the sequences and measurement techniques studied, the FS-SPGR sequence combined with the use of digitized image analysis provides the most accurate method for the assessment of ankle hyaline cartilage. (orig.). With 3 figs., 2 tabs.

MR imaging of articular cartilage in the ankle: comparison of available imaging sequences and methods of measurement in cadavers

International Nuclear Information System (INIS)

Tan, T.C.F.; Wilcox, D.M.; Frank, L.; Shih, C.; Trudell, D.J.; Sartoris, D.J.; Resnick, D.

1996-01-01

Objective. To assess hyaline cartilage of cadaveric ankles using different magnetic resonance (MR) imaging techniques and various methods of measurement. Design and patients. Cartilage thicknesses of the talus and tibia were measured in ten cadaveric ankles by naked eye and by digitized image analysis from MR images of fat-suppressed T1-weighted gradient recalled (FS-SPGR), sequences and pulsed transfer saturation sequences with (FS-STS) and without fat-suppression (STS); these measurements were compared with those derived from direct inspection of cadaveric sections. The accuracy and precision errors were evaluated statistically for each imaging technique as well as measuring method. Contrast-to-noise ratios of cartilage versus joint fluid and marrow were compared for each of the imaging sequences. Results. Statistically, measurements from FS-SPGR images were associated with the smallest estimation error. Precision error of measurements derived from digitized image analysis was found to be smaller than that derived from naked eye measurements. Cartilage thickness measurements in images from STS and FS-STS sequences revealed larger errors in both accuracy and precision. Interobserver variance was larger in naked eye assessment of the cartilage. Contrast-to-noise ratio of cartilage versus joint fluid and marrow was higher with FS-SPGR than with FS-STS or STS sequences. Conclusion. Of the sequences and measurement techniques studied, the FS-SPGR sequence combined with the use of digitized image analysis provides the most accurate method for the assessment of ankle hyaline cartilage. (orig.). With 3 figs., 2 tabs

Single-Trial Event-Related Potential Based Rapid Image Triage System

Directory of Open Access Journals (Sweden)

Ke Yu

2011-06-01

Full Text Available Searching for points of interest (POI in large-volume imagery is a challenging problem with few good solutions. In this work, a neural engineering approach called rapid image triage (RIT which could offer about a ten-fold speed up in POI searching is developed. It is essentially a cortically-coupled computer vision technique, whereby the user is presented bursts of images at a speed of 6–15 images per second and then neural signals called event-related potential (ERP is used as the ‘cue’ for user seeing images of high relevance likelihood. Compared to past efforts, the implemented system has several unique features: (1 it applies overlapping frames in image chip preparation, to ensure rapid image triage performance; (2 a novel common spatial-temporal pattern (CSTP algorithm that makes use of both spatial and temporal patterns of ERP topography is proposed for high-accuracy single-trial ERP detection; (3 a weighted version of probabilistic support-vector-machine (SVM is used to address the inherent unbalanced nature of single-trial ERP detection for RIT. High accuracy, fast learning, and real-time capability of the developed system shown on 20 subjects demonstrate the feasibility of a brainmachine integrated rapid image triage system for fast detection of POI from large-volume imagery.

Investigating the Feasibility of Rapid MRI for Image-Guided Motion Management in Lung Cancer Radiotherapy

Directory of Open Access Journals (Sweden)

Amit Sawant

2014-01-01

Full Text Available Cycle-to-cycle variations in respiratory motion can cause significant geometric and dosimetric errors in the administration of lung cancer radiation therapy. A common limitation of the current strategies for motion management is that they assume a constant, reproducible respiratory cycle. In this work, we investigate the feasibility of using rapid MRI for providing long-term imaging of the thorax in order to better capture cycle-to-cycle variations. Two nonsmall-cell lung cancer patients were imaged (free-breathing, no extrinsic contrast, and 1.5 T scanner. A balanced steady-state-free-precession (b-SSFP sequence was used to acquire cine-2D and cine-3D (4D images. In the case of Patient 1 (right midlobe lesion, ~40 mm diameter, tumor motion was well correlated with diaphragmatic motion. In the case of Patient 2, (left upper-lobe lesion, ~60 mm diameter, tumor motion was poorly correlated with diaphragmatic motion. Furthermore, the motion of the tumor centroid was poorly correlated with the motion of individual points on the tumor boundary, indicating significant rotation and/or deformation. These studies indicate that image quality and acquisition speed of cine-2D MRI were adequate for motion monitoring. However, significant improvements are required to achieve comparable speeds for truly 4D MRI. Despite several challenges, rapid MRI offers a feasible and attractive tool for noninvasive, long-term motion monitoring.

Compression and Processing of Space Image Sequences of Northern Lights and Sprites

DEFF Research Database (Denmark)

Forchhammer, Søren Otto; Martins, Bo; Jensen, Ole Riis

1999-01-01

Compression of image sequences of auroral activity as northern lights and thunderstorms with sprites is investigated.......Compression of image sequences of auroral activity as northern lights and thunderstorms with sprites is investigated....

Rapid volumetric imaging with Bessel-Beam three-photon microscopy

Science.gov (United States)

Chen, Bingying; Huang, Xiaoshuai; Gou, Dongzhou; Zeng, Jianzhi; Chen, Guoqing; Pang, Meijun; Hu, Yanhui; Zhao, Zhe; Zhang, Yunfeng; Zhou, Zhuan; Wu, Haitao; Cheng, Heping; Zhang, Zhigang; Xu, Chris; Li, Yulong; Chen, Liangyi; Wang, Aimin

2018-01-01

Owing to its tissue-penetration ability, multi-photon fluorescence microscopy allows for the high-resolution, non-invasive imaging of deep tissue in vivo; the recently developed three-photon microscopy (3PM) has extended the depth of high-resolution, non-invasive functional imaging of mouse brains to beyond 1.0 mm. However, the low repetition rate of femtosecond lasers that are normally used in 3PM limits the temporal resolution of point-scanning three-photon microscopy. To increase the volumetric imaging speed of 3PM, we propose a combination of an axially elongated needle-like Bessel-beam with three-photon excitation (3PE) to image biological samples with an extended depth of focus. We demonstrate the higher signal-to-background ratio (SBR) of the Bessel-beam 3PM compared to the two-photon version both theoretically and experimentally. Finally, we perform simultaneous calcium imaging of brain regions at different axial locations in live fruit flies and rapid volumetric imaging of neuronal structures in live mouse brains. These results highlight the unique advantage of conducting rapid volumetric imaging with a high SBR in the deep brain in vivo using scanning Bessel-3PM.

Image sequence analysis in nuclear medicine: (1) Parametric imaging using statistical modelling

International Nuclear Information System (INIS)

Liehn, J.C.; Hannequin, P.; Valeyre, J.

1989-01-01

This is a review of parametric imaging methods on Nuclear Medicine. A Parametric Image is an image in which each pixel value is a function of the value of the same pixel of an image sequence. The Local Model Method is the fitting of each pixel time activity curve by a model which parameter values form the Parametric Images. The Global Model Method is the modelling of the changes between two images. It is applied to image comparison. For both methods, the different models, the identification criterion, the optimization methods and the statistical properties of the images are discussed. The analysis of one or more Parametric Images is performed using 1D or 2D histograms. The statistically significant Parametric Images, (Images of significant Variances, Amplitudes and Differences) are also proposed [fr

MR imaging of the orbit and eye using inversion recovery sequences

International Nuclear Information System (INIS)

Smith, F.W.; Parekh, S.; Forrester, J.; Redpath, T.W.

1986-01-01

Most centers performing MR imaging use spin-echo sequences to produce images; however, there are many advantages to using short TI inversion-recovery sequences for examination of the orbits. By selecting a TI similar to the relaxation time of any structure, the signal from this can be suppressed, thereby enhancing the signal from other structures. Using a sequence of TR = 1,000 msec and TI of less than 200 msec, the signal from fat is suppressed, improving image quality adjacent to the surface coil and providing better contrast between orbital structures and fat. The use of this short TI sequence for the examination of the eye in patients with opaque lenses is an accurate method of diagnosis since the sequence enhances the signal from both long T1 and T2 lesions. Eighty-five patients with orbital or ocular pathology have been studied, and the results demonstrate the usefulness of this technique for diagnosis

Differential evolution optimization combined with chaotic sequences for image contrast enhancement

Energy Technology Data Exchange (ETDEWEB)

Santos Coelho, Leandro dos [Industrial and Systems Engineering Graduate Program, LAS/PPGEPS, Pontifical Catholic University of Parana, PUCPR Imaculada Conceicao, 1155, 80215-901 Curitiba, Parana (Brazil)], E-mail: leandro.coelho@pucpr.br; Sauer, Joao Guilherme [Industrial and Systems Engineering Graduate Program, LAS/PPGEPS, Pontifical Catholic University of Parana, PUCPR Imaculada Conceicao, 1155, 80215-901 Curitiba, Parana (Brazil)], E-mail: joao.sauer@gmail.com; Rudek, Marcelo [Industrial and Systems Engineering Graduate Program, LAS/PPGEPS, Pontifical Catholic University of Parana, PUCPR Imaculada Conceicao, 1155, 80215-901 Curitiba, Parana (Brazil)], E-mail: marcelo.rudek@pucpr.br

2009-10-15

Evolutionary Algorithms (EAs) are stochastic and robust meta-heuristics of evolutionary computation field useful to solve optimization problems in image processing applications. Recently, as special mechanism to avoid being trapped in local minimum, the ergodicity property of chaotic sequences has been used in various designs of EAs. Three differential evolution approaches based on chaotic sequences using logistic equation for image enhancement process are proposed in this paper. Differential evolution is a simple yet powerful evolutionary optimization algorithm that has been successfully used in solving continuous problems. The proposed chaotic differential evolution schemes have fast convergence rate but also maintain the diversity of the population so as to escape from local optima. In this paper, the image contrast enhancement is approached as a constrained nonlinear optimization problem. The objective of the proposed chaotic differential evolution schemes is to maximize the fitness criterion in order to enhance the contrast and detail in the image by adapting the parameters using a contrast enhancement technique. The proposed chaotic differential evolution schemes are compared with classical differential evolution to two testing images. Simulation results on three images show that the application of chaotic sequences instead of random sequences is a possible strategy to improve the performance of classical differential evolution optimization algorithm.

Fat-saturated diffusion-weighted imaging with three-dimensional MP-RAGE sequence

International Nuclear Information System (INIS)

Numano, Tomokazu; Homma, Kazuhiro; Takahashi, Nobuyuki; Hirose, Takeshi

2005-01-01

Image misrepresentation due to chemical shifts can create image artifacts on MR images. Distinguishing the organization and affected area can be difficult due to the chemical shift artifacts. Chemical shift selective (CHESS) is a method of decreasing chemical shift artifacts. In this study we have developed a new sequence for fat-saturated three-dimensional diffusion weighted MR imaging. This imaging was done during in vivo studies using an animal experiment MR imaging system at 2.0 T. In this sequence a preparation phase with a ''CHESS-90 deg RF-Motion Proving Gradient (MPG-180 deg RF-MPG-90 deg RF pulse train) was used to sensitize the magnetization to fat-saturated diffusion. Centric k-space acquisition order is necessary to minimize saturation effects from tissues with short relaxation times. From experimental results obtained with a phantom, the effect of the diffusion weighting and the effect of the fat-saturation were confirmed. From rat experimental results, fat-saturated diffusion weighted image data (0.55 x 0.55 x 0.55 mm 3 : voxel size) were obtained. This sequence was useful for in vivo imaging. (author)

Rapid Diagnostics of Onboard Sequences

Science.gov (United States)

Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

2012-01-01

Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

Geometrical primitives reconstruction from image sequence in an interactive context

International Nuclear Information System (INIS)

Monchal, L.; Aubry, P.

1995-01-01

We propose a method to recover 3D geometrical shape from image sequence, in a context of man machine co-operation. The human operator has to point out the edges of an object in the first image and choose a corresponding geometrical model. The algorithm tracks each relevant 2D segments describing surface discontinuities or limbs, in the images. Then, knowing motion of the camera between images, the positioning and the size of the virtual object are deduced by minimising a function. The function describes how well the virtual objects is linked to the extracted segments of the sequence, its geometrical model and pieces of information given by the operator. (author). 13 refs., 7 figs., 8 tabs

Hepatic adenomatosis: rapid sequence MR imaging following gadolinium enhancement: a case report

International Nuclear Information System (INIS)

Brummett, D.; Burton, E.M.; Sabio, H.

1999-01-01

Hepatic adenomas are primary liver tumors usually associated with underlying metabolic disease or with anabolic steroid or oral contraceptive use. Hepatic adenomatosis (HA) is defined as the presence of more than four adenomas. Only 13 cases of HA have been reported in patients without glycogen storage disease or steroid use. We report a case of HA imaged by postcontrast T1-weighted images obtained during a breath-holding series. The lesions were most conspicuous 3-4 min after contrast administration; 4 of the 5 tumors were not identified on T2-weighted images. Unlike previous reports of HA in which the lesions remained hyperintense during sequential postcontrast imaging, the smaller lesions in this case demonstrated contrast washout, thereby distinguishing them from hemangiomata. (orig.)

Optical flow estimation on image sequences with differently exposed frames

Science.gov (United States)

Bengtsson, Tomas; McKelvey, Tomas; Lindström, Konstantin

2015-09-01

Optical flow (OF) methods are used to estimate dense motion information between consecutive frames in image sequences. In addition to the specific OF estimation method itself, the quality of the input image sequence is of crucial importance to the quality of the resulting flow estimates. For instance, lack of texture in image frames caused by saturation of the camera sensor during exposure can significantly deteriorate the performance. An approach to avoid this negative effect is to use different camera settings when capturing the individual frames. We provide a framework for OF estimation on such sequences that contain differently exposed frames. Information from multiple frames are combined into a total cost functional such that the lack of an active data term for saturated image areas is avoided. Experimental results demonstrate that using alternate camera settings to capture the full dynamic range of an underlying scene can clearly improve the quality of flow estimates. When saturation of image data is significant, the proposed methods show superior performance in terms of lower endpoint errors of the flow vectors compared to a set of baseline methods. Furthermore, we provide some qualitative examples of how and when our method should be used.

Elimination of motion and pulsation artifacts using BLADE sequences in shoulder MR imaging

International Nuclear Information System (INIS)

Lavdas, E.; Zaloni, E.; Vlychou, M.; Vassiou, K.; Fezoulidis, I.; Tsagkalis, A.; Dailiana, Z.

2015-01-01

To evaluate the ability of proton-density with fat-suppression BLADE (proprietary name for periodically rotated overlapping parallel lines with enhanced reconstruction in MR systems from Siemens Healthcare, PDFS BLADE) and turbo inversion recovery magnitude-BLADE (TIRM BLADE) sequences to reduce motion and pulsation artifacts in shoulder magnetic resonance examinations. Forty-one consecutive patients who had been routinely scanned for shoulder examination participated in the study. The following pairs of sequences with and without BLADE were compared: (a) Oblique coronal proton-density sequence with fat saturation of 25 patients and (b) oblique sagittal T2 TIRM-weighed sequence of 20 patients. Qualitative analysis was performed by two experienced radiologists. Image motion and pulsation artifacts were also evaluated. In oblique coronal PDFS BLADE sequences, motion artifacts have been significantly eliminated, even in five cases of non-diagnostic value with conventional imaging. Similarly, in oblique sagittal T2 TIRM BLADE sequences, image quality has been improved, even in six cases of non-diagnostic value with conventional imaging. Furthermore, flow artifacts have been improved in more than 80% of all the cases. The use of BLADE sequences is recommended in shoulder imaging, especially in uncooperative patients because it effectively eliminates motion and pulsation artifacts. (orig.)

Visualization and correction of automated segmentation, tracking and lineaging from 5-D stem cell image sequences.

Science.gov (United States)

Wait, Eric; Winter, Mark; Bjornsson, Chris; Kokovay, Erzsebet; Wang, Yue; Goderie, Susan; Temple, Sally; Cohen, Andrew R

2014-10-03

Neural stem cells are motile and proliferative cells that undergo mitosis, dividing to produce daughter cells and ultimately generating differentiated neurons and glia. Understanding the mechanisms controlling neural stem cell proliferation and differentiation will play a key role in the emerging fields of regenerative medicine and cancer therapeutics. Stem cell studies in vitro from 2-D image data are well established. Visualizing and analyzing large three dimensional images of intact tissue is a challenging task. It becomes more difficult as the dimensionality of the image data increases to include time and additional fluorescence channels. There is a pressing need for 5-D image analysis and visualization tools to study cellular dynamics in the intact niche and to quantify the role that environmental factors play in determining cell fate. We present an application that integrates visualization and quantitative analysis of 5-D (x,y,z,t,channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. We combine unsupervised image

Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.

Directory of Open Access Journals (Sweden)

Teresa Nogueira

Full Text Available Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.

MR imaging of the temporomandibular joint. Part 2. Effect of flip angle on MR imaging with FLASH sequence

International Nuclear Information System (INIS)

Sakamoto, Maya; Sasano, Takashi; Higano, Shuichi; Takahashi, Shoki; Kurihara, Noriko

1998-01-01

In our previous study on MR imaging of the temporomandibular joint (TMJ), fast low angle shot (FLASH) showed the highest image contrast between disc and surrounding TMJ tissues compared with those of 4 other sequences (i,e., fast imaging with steady precession (FISP), conventional T1-weighted spin echo (SE) and fast spin echo (FSE, TR/TE/ETL: 1100/12/3, 3000/15/7)). Furthermore, FLASH also received a high score on visual evaluation including the position and contour of the disc, and the border between the disc and surrounding tissues. Therefore, we concluded that FLASH was the most suitable sequence for evaluating the TMJ disc. However, the image contrast and signal intensity on MR imaging with gradient echo pulse sequence are affected by flip angle. Consequently, in this report, to find the most suitable flip angle for MR scanning of the TMJ using a FLASH sequence (TR/TE: 450/11), ten TMJs of 5 volunteers were experimentally imaged with various flip angles from 10 degrees to 70 degrees at an interval of 10 degrees between 10 to 70. The image contrast and contrast-to-noise ratio (CNR) between the disc and surrounding tissues were compared. In addition, signal-to-noise ratio (SNR) of phantoms was also calculated using the same imaging parameters. Visual evaluation including position and contour of the disc, and the border between the disc and surrounding tissues, was also performed by 4 radiologists. As the flip angle increased, imaging contrast decreased while SNR increased. Images with flip angles between 30 and 60 degrees demonstrated high CNR. On visual evaluation, images using flip angles between 30 and 50 degrees received high scores. In conclusion, FLASH sequence with a flip angle between 30 and 50 degrees was considered most suitable for evaluating the TMJ disc based on the results of visual assessment and analysis of three major components of image diagnostic quality: image contrast, CNR and SNR. (author)

Optimal pulse sequence for ferumoxides-enhanced MR imaging used in the detection of hepatocellular carcinoma: a comparative study using seven pulse sequences

International Nuclear Information System (INIS)

Kim, Seung Hoon; Choi, Dongil; Lim, Jae Hoon; Lee, Won Jae; Jang, Hyun Jung; Lim, Kyo Keun; Lee, Soon Jin; Cho, Jae Min; Kim, Seung Kwon; Kim, Gab Chul

2002-01-01

To identify the optimal pulse sequence for ferumoxides-enhanced magnetic resonance (MR) imaging in the detection of hepatocelluar carcinomas (HCCs). Sixteen patients with 25 HCCs underwent MR imaging following intravenous infusion of ferumoxides. All MR studies were performed on a 1.5-T MR system, using a phased-array coil. Ferumoxides (Feridex IV) at a dose of 15 μmol/Kg was slowly infused intravenously, and axial images of seven sequences were obtained 30 minutes after the end of infusion. The MR protocol included fast spin-echo (FSE) with two echo times (TR3333-8571/TE18 and 90-117), singleshot FSE (SSFSE) with two echo times (TR∞/TE39 and 98), T2-weighted gradient-recalled acquisition in the steady state (GRASS) (TR216/TE20), T2-weighted fast multiplanar GRASS (FMPGR) (TR130/TE8.4-9.5), and T2-weighted fast multiplanar spoiled GRASS (FMPSPGR) (TR130/TE8.4-9.5). Contrast-to-noise ratios (CNRs) of HCCs determined during the imaging sequences formed the basis of quantitative analysis, and images were qualitatively assessed in terms of lesion conspicuity and image artifacts. The diagnostic accuracy of all sequences was assessed using receiver operating characteristic (ROC) analysis. Quantitative analysis revealed that the CNRs of T2-weighted FMPGR and T2-weighted FMPSPGR were significantly higher than those of the other sequences, while qualitative analysis showed that image artifacts were prominent at T2-weighted GRASS imaging. Lesion conspicuity was statistically significantly less clear at SSFSE imaging. In term of lesion detection, T-weighted FMPGR, T2- weighted FMPSPGR, and proton density FSE imaging were statistically superior to the others. T2-weighted FMPGR, T2- weighted FMPSPGR, and proton density FSE appear to be the optimal pulse sequences for ferumoxidesenhanced MR imaging in the detection of HCCs

An Extended Multilocus Sequence Typing (MLST) Scheme for Rapid Direct Typing of Leptospira from Clinical Samples

OpenAIRE

Weiss, Sabrina; Menezes, Angela; Woods, Kate; Chanthongthip, Anisone; Dittrich, Sabine; Opoku-Boateng, Agatha; Kimuli, Maimuna; Chalker, Victoria

2016-01-01

Background Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST) data direct from patient specimens while minimising costs for subsequent sequencing. Methodology and Findings An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen t...

Intubation conditions after rocuronium or succinylcholine for rapid sequence induction with alfentanil and propofol in the emergency patient

DEFF Research Database (Denmark)

Larsen, P B; Hansen, E G; Jacobsen, L S

2005-01-01

Background and objective: Previous studies mainly conducted on elective patients recommend doses of 0.9-1.2 mg kg[-1] rocuronium to obtain comparable intubation conditions with succinylcholine 1.0 mg kg[-1] after 60 s during a rapid-sequence induction. We decided to compare the overall intubating...... conditions of standard doses of rocuronium 0.6 mg kg[-1] and succinylcholine 1.0 mg kg[-1] during a strict rapid-sequence induction regimen including propofol and alfentanil. Methods: Male and female patients (ASA I-III) older than 17 yr scheduled for emergency abdominal or gynaecological surgery...... and with increased risk of pulmonary aspiration of gastric content were randomized to a rapid-sequence induction with succinylcholine 1.0 mg kg[-1] or rocuronium 0.6 mg kg[-1]. Patients with a predicted difficult airway were excluded. A senior anaesthesiologist 'blinded' for the randomization performed...

Optimal pulse-sequence parameters for MR imaging of the immature brain

International Nuclear Information System (INIS)

Nowell, M.A.; Hackney, D.B.; Zimmerman, R.A.; Bilaniuk, L.T.; Grossman, R.I.; Goldberg, H.I.

1986-01-01

Appropriate spin-echo pulse sequence parameters generate MR images with very high gray matter/white matter contrast in neonates and young infants. Low-contrast images appear to result from utilization of ''adult-type'' parameters to investigate tissues that have relaxation characteristics quite different than those of adult brain. In these young patients long spin-echo sequences with repetition times of 3,000-3,500 msec and multiple echoes with the longest echo time set at 120-160 msec are employed to yield high-contrast ''T2-weighted'' images

Real-time UAV trajectory generation using feature points matching between video image sequences

Science.gov (United States)

Byun, Younggi; Song, Jeongheon; Han, Dongyeob

2017-09-01

Unmanned aerial vehicles (UAVs), equipped with navigation systems and video capability, are currently being deployed for intelligence, reconnaissance and surveillance mission. In this paper, we present a systematic approach for the generation of UAV trajectory using a video image matching system based on SURF (Speeded up Robust Feature) and Preemptive RANSAC (Random Sample Consensus). Video image matching to find matching points is one of the most important steps for the accurate generation of UAV trajectory (sequence of poses in 3D space). We used the SURF algorithm to find the matching points between video image sequences, and removed mismatching by using the Preemptive RANSAC which divides all matching points to outliers and inliers. The inliers are only used to determine the epipolar geometry for estimating the relative pose (rotation and translation) between image sequences. Experimental results from simulated video image sequences showed that our approach has a good potential to be applied to the automatic geo-localization of the UAVs system

Prostate cancer in magnetic resonance imaging: diagnostic utilites of spectroscopic sequences

International Nuclear Information System (INIS)

Caivano, Rocchina; Cirillo, Patrizia; Lotumolo, Antonella; Fortunato, Giovanna; Zandolino, Alexis; Cammarota, Aldo; Balestra, Antonio; Macarini, Luca; Vita, Giulia

2012-01-01

The aim of our work is to determine the efficacy of a combined study 3 Tesla Magnetic Resonance Imaging (3T MRI), with phased-array coil, for the detection of prostate cancer using magnetic resonance spectroscopy (MRS) and diffusion-weighted images (DWI) in identifying doubt nodules. In this study, we prospectively studied 46 patients who consecutively underwent digital-rectal exploration for high doses of prostate specific antigen (PSA), as well as a MRI examination and a subsequent rectal biopsy. The study of magnetic resonance imaging was performed with a Philips Achieva 3T scanner and phased-array coil. The images were obtained with turbo spin-echo sequences T2-weighted images, T1-weighted before and after the administration of contrast medium, DWI sequences and 3D spectroscopic sequences. The ultrasound-guided prostate biopsy was performed approximately 15 days after the MRI. The data obtained from MR images and spectroscopy were correlated with histological data. MRI revealed sensitivity and specificity of 88% and 61% respectively and positive predictive value (PPV) of 73%, negative predicted value (NPV) of 81% and accuracy of 76%. In identifying the location of prostate cancer, the sensitivity of 3T MRS was 92%, with a specificity of 89%, PPV of 87%, NPV of 88% and accuracy of 87%; DWI showed a sensitivity of 88%, specificity of 61%, PPV of 73%, NPV of 81% and accuracy of 76%. The 3T MR study with phased-array coil and the use of DWI and spectroscopic sequences, in addition to T2-weighted sequences, revealed to be accurate in the diagnosis of prostate cancer and in the identification of nodules to be biopsied. It may be indicated as a resolute way before biopsy in patients with elevated PSA value and can be proposed in the staging and follow-up.

Spatiotemporal reconstruction of the Aquilegia rapid radiation through next-generation sequencing of rapidly evolving cpDNA regions.

Science.gov (United States)

Fior, Simone; Li, Mingai; Oxelman, Bengt; Viola, Roberto; Hodges, Scott A; Ometto, Lino; Varotto, Claudio

2013-04-01

Aquilegia is a well-known model system in the field of evolutionary biology, but obtaining a resolved and well-supported phylogenetic reconstruction for the genus has been hindered by its recent and rapid diversification. Here, we applied 454 next-generation sequencing to PCR amplicons of 21 of the most rapidly evolving regions of the plastome to generate c. 24 kb of sequences from each of 84 individuals from throughout the genus. The resulting phylogeny has well-supported resolution of the main lineages of the genus, although recent diversification such as in the European taxa remains unresolved. By producing a chronogram of the whole Ranunculaceae family based on published data, we inferred calibration points for dating the Aquilegia radiation. The genus originated in the upper Miocene c. 6.9 million yr ago (Ma) in Eastern Asia, and diversification occurred c. 4.8 Ma with the split of two main clades, one colonizing North America, and the other Western Eurasia through the mountains of Central Asia. This was followed by a back-to-Asia migration, originating from the European stock using a North Asian route. These results provide the first backbone phylogeny and spatiotemporal reconstruction of the Aquilegia radiation, and constitute a robust framework to address the adaptative nature of speciation within the group. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Realise : reconstruction of reality from image sequences

NARCIS (Netherlands)

Leymarie, F.; de la Fortelle, A.; Koenderink, Jan J.; Kappers, A. M L; Stavridi, M.; van Ginneken, B.; Muller, S.; Krake, S.; Faugeras, O.; Robert, L.; Gauclin, C.; Laveau, S.; Zeller, C.; Anon,

1996-01-01

REALISE has for principal goals to extract from sequences of images, acquired with a moving camera, information necessary for determining the 3D (CAD-like) structure of a real-life scene together with information about the radiometric signatures of surfaces bounding the extracted 3D objects (e.g.

Research on Image Encryption Based on DNA Sequence and Chaos Theory

Science.gov (United States)

Tian Zhang, Tian; Yan, Shan Jun; Gu, Cheng Yan; Ren, Ran; Liao, Kai Xin

2018-04-01

Nowadays encryption is a common technique to protect image data from unauthorized access. In recent years, many scientists have proposed various encryption algorithms based on DNA sequence to provide a new idea for the design of image encryption algorithm. Therefore, a new method of image encryption based on DNA computing technology is proposed in this paper, whose original image is encrypted by DNA coding and 1-D logistic chaotic mapping. First, the algorithm uses two modules as the encryption key. The first module uses the real DNA sequence, and the second module is made by one-dimensional logistic chaos mapping. Secondly, the algorithm uses DNA complementary rules to encode original image, and uses the key and DNA computing technology to compute each pixel value of the original image, so as to realize the encryption of the whole image. Simulation results show that the algorithm has good encryption effect and security.

Retrieval of Sentence Sequences for an Image Stream via Coherence Recurrent Convolutional Networks.

Science.gov (United States)

Park, Cesc Chunseong; Kim, Youngjin; Kim, Gunhee

2018-04-01

We propose an approach for retrieving a sequence of natural sentences for an image stream. Since general users often take a series of pictures on their experiences, much online visual information exists in the form of image streams, for which it would better take into consideration of the whole image stream to produce natural language descriptions. While almost all previous studies have dealt with the relation between a single image and a single natural sentence, our work extends both input and output dimension to a sequence of images and a sequence of sentences. For retrieving a coherent flow of multiple sentences for a photo stream, we propose a multimodal neural architecture called coherence recurrent convolutional network (CRCN), which consists of convolutional neural networks, bidirectional long short-term memory (LSTM) networks, and an entity-based local coherence model. Our approach directly learns from vast user-generated resource of blog posts as text-image parallel training data. We collect more than 22 K unique blog posts with 170 K associated images for the travel topics of NYC, Disneyland , Australia, and Hawaii. We demonstrate that our approach outperforms other state-of-the-art image captioning methods for text sequence generation, using both quantitative measures and user studies via Amazon Mechanical Turk.

Algorithms for detection of objects in image sequences captured from an airborne imaging system

Science.gov (United States)

Kasturi, Rangachar; Camps, Octavia; Tang, Yuan-Liang; Devadiga, Sadashiva; Gandhi, Tarak

1995-01-01

This research was initiated as a part of the effort at the NASA Ames Research Center to design a computer vision based system that can enhance the safety of navigation by aiding the pilots in detecting various obstacles on the runway during critical section of the flight such as a landing maneuver. The primary goal is the development of algorithms for detection of moving objects from a sequence of images obtained from an on-board video camera. Image regions corresponding to the independently moving objects are segmented from the background by applying constraint filtering on the optical flow computed from the initial few frames of the sequence. These detected regions are tracked over subsequent frames using a model based tracking algorithm. Position and velocity of the moving objects in the world coordinate is estimated using an extended Kalman filter. The algorithms are tested using the NASA line image sequence with six static trucks and a simulated moving truck and experimental results are described. Various limitations of the currently implemented version of the above algorithm are identified and possible solutions to build a practical working system are investigated.

Frequency-locked pulse sequencer for high-frame-rate monochromatic tissue motion imaging.

Science.gov (United States)

Azar, Reza Zahiri; Baghani, Ali; Salcudean, Septimiu E; Rohling, Robert

2011-04-01

To overcome the inherent low frame rate of conventional ultrasound, we have previously presented a system that can be implemented on conventional ultrasound scanners for high-frame-rate imaging of monochromatic tissue motion. The system employs a sector subdivision technique in the sequencer to increase the acquisition rate. To eliminate the delays introduced during data acquisition, a motion phase correction algorithm has also been introduced to create in-phase displacement images. Previous experimental results from tissue- mimicking phantoms showed that the system can achieve effective frame rates of up to a few kilohertz on conventional ultrasound systems. In this short communication, we present a new pulse sequencing strategy that facilitates high-frame-rate imaging of monochromatic motion such that the acquired echo signals are inherently in-phase. The sequencer uses the knowledge of the excitation frequency to synchronize the acquisition of the entire imaging plane to that of an external exciter. This sequencing approach eliminates any need for synchronization or phase correction and has applications in tissue elastography, which we demonstrate with tissue-mimicking phantoms. © 2011 IEEE

Small-target leak detection for a closed vessel via infrared image sequences

Science.gov (United States)

Zhao, Ling; Yang, Hongjiu

2017-03-01

This paper focus on a leak diagnosis and localization method based on infrared image sequences. Some problems on high probability of false warning and negative affect for marginal information are solved by leak detection. An experimental model is established for leak diagnosis and localization on infrared image sequences. The differential background prediction is presented to eliminate the negative affect of marginal information on test vessel based on a kernel regression method. A pipeline filter based on layering voting is designed to reduce probability of leak point false warning. A synthesize leak diagnosis and localization algorithm is proposed based on infrared image sequences. The effectiveness and potential are shown for developed techniques through experimental results.

COMPARISON OF ROCURONIUM BROMIDE AND SUCCINYLCHOLINE CHLORIDE FOR USE DURING RAPID SEQUENCE INTUBATION IN ADULTS

Directory of Open Access Journals (Sweden)

Ch. Penchalaiah

2015-08-01

Full Text Available BACKGROUND AND OBJECTIVE : The goal of rapid sequence intubation is to secure the patients airway smoothly and quickly, minimizing the chances of regurgitation and aspiration of gastric contents. Traditionally succinylcholine chloride has been the neuromuscular blocking drug of choi ce for use in rapid sequence intubation because of its rapid onset of action and profound relaxation. Succinylcholine chloride remains unsurpassed in providing ideal intubating conditions. However the use of succinylcholine chloride is associated with many side effects like muscle pain, bradycardia, hyperkalaemia and rise in intragastric and intraocular pressure. Rocuronium bromide is the only drug currently available which has the rapidity of onset of action like succinylcholine chloride. Hence the present study was undertaken to compare rocuronium bromide with succinylcholine chloride for use during rapid sequence intubation in adult patients. METHODOLOGY : The study population consisted of 90 patients aged between 18 - 60 years posted for various elective su rgeries requiring general anaesthesia . S tudy population was randomly divided into 3 groups with 30 patients in each sub group. 1. Group I : Intubated with 1 mg kg - 1 of succinylcholine chloride (n=30 . 2. Grou p II : Intubated with rocuronium bromide 0.6 mg kg - 1 (n=30 . 3. Group III : Intubated with rocuronium bromide 0.9 mg kg - 1 (n=30 . Intubating conditions were assessed at 60 seconds based on the scale adopted by Toni Magorian et al. 1993. The haemodynamic para meters in the present study were compared using p - value obtained from student t - test . RESULTS : It was noted that succinylcholine chloride 1 mg kg - 1 body weight produced excellent intubating conditions in all patients. Rocuronium bromide 0.6 mg kg - 1 body we ight produced excellent intubating conditions in 53.33% of patients but produced good to excellent intubating conditions in 96.67% of patients. Rocuronium bromide 0.9 mg kg - 1

Rapid development of medical imaging tools with open-source libraries.

Science.gov (United States)

Caban, Jesus J; Joshi, Alark; Nagy, Paul

2007-11-01

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

Rapid Sanger sequencing of the 16S rRNA gene for identification of some common pathogens.

Directory of Open Access Journals (Sweden)

Linxiang Chen

Full Text Available Conventional Sanger sequencing remains time-consuming and laborious. In this study, we developed a rapid improved sequencing protocol of 16S rRNA for pathogens identification by using a new combination of SYBR Green I real-time PCR and Sanger sequencing with FTA® cards. To compare the sequencing quality of this method with conventional Sanger sequencing, 12 strains, including three kinds of strains (1 reference strain and 3 clinical strains, which were previously identified by biochemical tests, which have 4 Pseudomonas aeruginosa, 4 Staphyloccocus aureus and 4 Escherichia coli, were targeted. Additionally, to validate the sequencing results and bacteria identification, expanded specimens with 90 clinical strains, also comprised of the three kinds of strains which included 30 samples respectively, were performed as just described. The results showed that although statistical differences (P<0.05 were found in sequencing quality between the two methods, their identification results were all correct and consistent. The workload, the time consumption and the cost per batch were respectively light versus heavy, 8 h versus 11 h and $420 versus $400. In the 90 clinical strains, all of the Pseudomonas aeruginosa and Staphyloccocus aureus strains were correctly identified, but only 26.7% of the Escherichia coli strains were recognized as Escherichia coli, while 33.3% as Shigella sonnei and 40% as Shigella dysenteriae. The protocol described here is a rapid, reliable, stable and convenient method for 16S rRNA sequencing, and can be used for Pseudomonas aeruginosa and Staphyloccocus aureus identification, yet it is not completely suitable for discriminating Escherichia coli and Shigella strains.

RapidEye constellation relative radiometric accuracy measurement using lunar images

Science.gov (United States)

Steyn, Joe; Tyc, George; Beckett, Keith; Hashida, Yoshi

2009-09-01

The RapidEye constellation includes five identical satellites in Low Earth Orbit (LEO). Each satellite has a 5-band (blue, green, red, red-edge and near infrared (NIR)) multispectral imager at 6.5m GSD. A three-axes attitude control system allows pointing the imager of each satellite at the Moon during lunations. It is therefore possible to image the Moon from near identical viewing geometry within a span of 80 minutes with each one of the imagers. Comparing the radiometrically corrected images obtained from each band and each satellite allows a near instantaneous relative radiometric accuracy measurement and determination of relative gain changes between the five imagers. A more traditional terrestrial vicarious radiometric calibration program has also been completed by MDA on RapidEye. The two components of this program provide for spatial radiometric calibration ensuring that detector-to-detector response remains flat, while a temporal radiometric calibration approach has accumulated images of specific dry dessert calibration sites. These images are used to measure the constellation relative radiometric response and make on-ground gain and offset adjustments in order to maintain the relative accuracy of the constellation within +/-2.5%. A quantitative comparison between the gain changes measured by the lunar method and the terrestrial temporal radiometric calibration method is performed and will be presented.

Rapid sequence induction has no use in pediatric anesthesia.

Science.gov (United States)

Engelhardt, Thomas

2015-01-01

(Classic) rapid sequence induction and intubation (RSII) has been considered fundamental to the provision of safe anesthesia. This technique consists of a combination of drugs and techniques and is intended to prevent pulmonary aspiration of gastric content with catastrophic outcomes to the patient. This review investigates aspects of this technique and highlights dangers and frauds if this technique is transferred directly into pediatric anesthesia practice. The author recommends a controlled anesthesia induction by trained pediatric anesthesiologist with suitable equipment for the children considered at risk of pulmonary aspiration. RSSI is a dangerous technique if adopted without modification into pediatric anesthesia and has in its 'classic' form no use. © 2014 John Wiley & Sons Ltd.

Contrast-enhanced dynamic MR imaging of parasellar tumor using fast spin-echo sequence

International Nuclear Information System (INIS)

Kusunoki, Katsusuke; Ohue, Shiro; Ichikawa, Haruhisa; Saito, Masahiro; Sadamoto, Kazuhiko; Sakaki, Saburo; Miki, Hitoshi.

1995-01-01

We have applied a new dynamic MRI technique that uses a fast spin-echo sequence to parasellar tumors. This sequence has less susceptible effect and better spatial resolution than a gradient echo sequence, providing faster images than a short spin-echo sequence does. Image was obtained in the coronal or sagittal plane using a 1.5T clinical MRI system, and then, dynamic MR images were acquired every 10 to 20 sec after administration of Gd-DTPA (0.1 mmol/kg). The subjects were 12 patients (5 microadenomas, 5 macroadenomas and 2 Rathke's cleft cysts) and 5 normal volunteers. As for volunteers, the cavernous sinus, pituitary stalk and posterior pituitary gland were contrasted on the first image, followed by visualization of the proximal portion adjacent to the junction of the infundibulum and the anterior pituitary gland, and finally by contrasting the distal portion of the anterior pituitary gland. There was a difference with respect to tumor contrast between microadenomas and macroadenomas. In the case of the macroadenomas, the tumor was contrasted at the same time as, or faster than the anterior pituitary gland, while with the microadenomas the tumor was enhanced later than the anterior pituitary gland. No enhancement with contrast medium was seen in Rathke's cleft cysts. In addition, it was possible to differentiate a recurrent tumor from a piece of muscle placed at surgery since the images obtained by the fast spin-echo sequence were clearer than those obtained by gradient echo sequence. (author)

Imaging cardiac activation sequence during ventricular tachycardia in a canine model of nonischemic heart failure.

Science.gov (United States)

Han, Chengzong; Pogwizd, Steven M; Yu, Long; Zhou, Zhaoye; Killingsworth, Cheryl R; He, Bin

2015-01-15

Noninvasive cardiac activation imaging of ventricular tachycardia (VT) is important in the clinical diagnosis and treatment of arrhythmias in heart failure (HF) patients. This study investigated the ability of the three-dimensional cardiac electrical imaging (3DCEI) technique for characterizing the activation patterns of spontaneously occurring and norepinephrine (NE)-induced VTs in a newly developed arrhythmogenic canine model of nonischemic HF. HF was induced by aortic insufficiency followed by aortic constriction in three canines. Up to 128 body-surface ECGs were measured simultaneously with bipolar recordings from up to 232 intramural sites in a closed-chest condition. Data analysis was performed on the spontaneously occurring VTs (n=4) and the NE-induced nonsustained VTs (n=8) in HF canines. Both spontaneously occurring and NE-induced nonsustained VTs initiated by a focal mechanism primarily from the subendocardium, but occasionally from the subepicardium of left ventricle. Most focal initiation sites were located at apex, right ventricular outflow tract, and left lateral wall. The NE-induced VTs were longer, more rapid, and had more focal sites than the spontaneously occurring VTs. Good correlation was obtained between imaged activation sequence and direct measurements (averaged correlation coefficient of ∼0.70 over 135 VT beats). The reconstructed initiation sites were ∼10 mm from measured initiation sites, suggesting good localization in such a large animal model with cardiac size similar to a human. Both spontaneously occurring and NE-induced nonsustained VTs had focal initiation in this canine model of nonischemic HF. 3DCEI is feasible to image the activation sequence and help define arrhythmia mechanism of nonischemic HF-associated VTs. Copyright © 2015 the American Physiological Society.

Motion Estimation Using the Firefly Algorithm in Ultrasonic Image Sequence of Soft Tissue

Directory of Open Access Journals (Sweden)

Chih-Feng Chao

2015-01-01

Full Text Available Ultrasonic image sequence of the soft tissue is widely used in disease diagnosis; however, the speckle noises usually influenced the image quality. These images usually have a low signal-to-noise ratio presentation. The phenomenon gives rise to traditional motion estimation algorithms that are not suitable to measure the motion vectors. In this paper, a new motion estimation algorithm is developed for assessing the velocity field of soft tissue in a sequence of ultrasonic B-mode images. The proposed iterative firefly algorithm (IFA searches for few candidate points to obtain the optimal motion vector, and then compares it to the traditional iterative full search algorithm (IFSA via a series of experiments of in vivo ultrasonic image sequences. The experimental results show that the IFA can assess the vector with better efficiency and almost equal estimation quality compared to the traditional IFSA method.

A comparative analysis of double inversion recovery TFE and TSE sequences on carotid artery wall imaging

International Nuclear Information System (INIS)

Chen Jun; Di Yujin; Bu Chunqing; Zhang Yanfeng; Li Shuhua

2012-01-01

Objective: To analyze the characteristics of double inversion recovery (DIR) turbo field echo (TFE) and turbo spin echo (TSE) sequences and explore the value of double inversion recovery TFE sequence on carotid artery wall imaging. Patients and methods: 56 patients (32 males and 24 females, aged 31–76 years with a mean age of 53 years) were performed with DIR TFE and DIR TSE T1 weighted imaging (T1WI) sequences on carotid artery bifurcations. Image quality acquired by different techniques were evaluated and scored by two physicians. Whether there is significant difference is determined by SPSS 11.0 software. Paired-samples t test was used for statistics. Results: There was no significant difference in the image quality scores between two sequences (t = 0.880, P = 0.383 > 0.05). Conclusions: DIR TFE sequence has short scanning time and high spatial resolution. DIR TFE sequence can be used as the preferred sequence for screening carotid atherosclerotic plaque compared with DIR TSE sequence.

Safety Assessment of Advanced Imaging Sequences II: Simulations

DEFF Research Database (Denmark)

Jensen, Jørgen Arendt

2016-01-01

.6%, when using the impulse response of the probe estimated from an independent measurement. The accuracy is increased to between -22% to 24.5% for MI and between -33.2% to 27.0% for Ispta.3, when using the pressure response measured at a single point to scale the simulation. The spatial distribution of MI...... Mechanical Index (MI) and Ispta.3 as required by FDA. The method is performed on four different imaging schemes and compared to measurements conducted using the SARUS experimental scanner. The sequences include focused emissions with an F-number of 2 with 64 elements that generate highly non-linear fields....... The simulation time is between 0.67 ms to 2.8 ms per emission and imaging point, making it possible to simulate even complex emission sequences in less than 1 s for a single spatial position. The linear simulations yield a relative accuracy on MI between -12.1% to 52.3% and for Ispta.3 between -38.6% to 62...

Rapid evaluation and quality control of next generation sequencing data with FaQCs.

Science.gov (United States)

Lo, Chien-Chi; Chain, Patrick S G

2014-11-19

Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform's sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects. Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics. FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

Meteor localization via statistical analysis of spatially temporal fluctuations in image sequences

Science.gov (United States)

Kukal, Jaromír.; Klimt, Martin; Šihlík, Jan; Fliegel, Karel

2015-09-01

Meteor detection is one of the most important procedures in astronomical imaging. Meteor path in Earth's atmosphere is traditionally reconstructed from double station video observation system generating 2D image sequences. However, the atmospheric turbulence and other factors cause spatially-temporal fluctuations of image background, which makes the localization of meteor path more difficult. Our approach is based on nonlinear preprocessing of image intensity using Box-Cox and logarithmic transform as its particular case. The transformed image sequences are then differentiated along discrete coordinates to obtain statistical description of sky background fluctuations, which can be modeled by multivariate normal distribution. After verification and hypothesis testing, we use the statistical model for outlier detection. Meanwhile the isolated outlier points are ignored, the compact cluster of outliers indicates the presence of meteoroids after ignition.

Comparison of 3 T and 7 T MRI clinical sequences for ankle imaging

Energy Technology Data Exchange (ETDEWEB)

Juras, Vladimir, E-mail: vladimir.juras@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Slovak Academy of Sciences, Institute of Measurement Science, Dubravska cesta 9, 84104 Bratislava (Slovakia); Welsch, Goetz, E-mail: welsch@bwh.harvard.edu [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Baer, Peter, E-mail: baerpeter@siemens.com [Siemens Healthcare, Richard-Strauss-Strasse 76, D81679 Munich (Germany); Kronnerwetter, Claudia, E-mail: claudia.kronnerwetter@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Fujita, Hiroyuki, E-mail: hiroyuki.fujita@qualedyn.com [Quality Electrodynamics, LCC, 777 Beta Dr, Cleveland, OH 44143-2336 (United States); Trattnig, Siegfried, E-mail: siegfried.trattnig@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria)

2012-08-15

The purpose of this study was to compare 3 T and 7 T signal-to-noise and contrast-to noise ratios of clinical sequences for imaging of the ankles with optimized sequences and dedicated coils. Ten healthy volunteers were examined consecutively on both systems with three clinical sequences: (1) 3D gradient-echo, T{sub 1}-weighted; (2) 2D fast spin-echo, PD-weighted; and (3) 2D spin-echo, T{sub 1}-weighted. SNR was calculated for six regions: cartilage; bone; muscle; synovial fluid; Achilles tendon; and Kager's fat-pad. CNR was obtained for cartilage/bone, cartilage/fluid, cartilage/muscle, and muscle/fat-pad, and compared by a one-way ANOVA test for repeated measures. Mean SNR significantly increased at 7 T compared to 3 T for 3D GRE, and 2D TSE was 60.9% and 86.7%, respectively. In contrast, an average SNR decrease of almost 25% was observed in the 2D SE sequence. A CNR increase was observed in 2D TSE images, and in most 3D GRE images. There was a substantial benefit from ultra high-field MR imaging of ankles with routine clinical sequences at 7 T compared to 3 T. Higher SNR and CNR at ultra-high field MR scanners may be useful in clinical practice for ankle imaging. However, carefully optimized protocols and dedicated extremity coils are necessary to obtain optimal results.

Artificial Intelligence In Processing A Sequence Of Time-Varying Images

Science.gov (United States)

Siler, W.; Tucker, D.; Buckley, J.; Hess, R. G.; Powell, V. G.

1985-04-01

A computer system is described for unsupervised analysis of five sets of ultrasound images of the heart. Each set consists of 24 frames taken at 33 millisecond intervals. The images are acquired in real time with computer control of the ultrasound apparatus. After acquisition the images are segmented by a sequence of image-processing programs; features are extracted and stored in a version of the Carnegie- Mellon Blackboard. Region classification is accomplished by a fuzzy logic expert system FLOPS based on OPS5. Preliminary results are given.

Rapid whole genome sequencing and precision neonatology.

Science.gov (United States)

Petrikin, Joshua E; Willig, Laurel K; Smith, Laurie D; Kingsmore, Stephen F

2015-12-01

Traditionally, genetic testing has been too slow or perceived to be impractical to initial management of the critically ill neonate. Technological advances have led to the ability to sequence and interpret the entire genome of a neonate in as little as 26 h. As the cost and speed of testing decreases, the utility of whole genome sequencing (WGS) of neonates for acute and latent genetic illness increases. Analyzing the entire genome allows for concomitant evaluation of the currently identified 5588 single gene diseases. When applied to a select population of ill infants in a level IV neonatal intensive care unit, WGS yielded a diagnosis of a causative genetic disease in 57% of patients. These diagnoses may lead to clinical management changes ranging from transition to palliative care for uniformly lethal conditions for alteration or initiation of medical or surgical therapy to improve outcomes in others. Thus, institution of 2-day WGS at time of acute presentation opens the possibility of early implementation of precision medicine. This implementation may create opportunities for early interventional, frequently novel or off-label therapies that may alter disease trajectory in infants with what would otherwise be fatal disease. Widespread deployment of rapid WGS and precision medicine will raise ethical issues pertaining to interpretation of variants of unknown significance, discovery of incidental findings related to adult onset conditions and carrier status, and implementation of medical therapies for which little is known in terms of risks and benefits. Despite these challenges, precision neonatology has significant potential both to decrease infant mortality related to genetic diseases with onset in newborns and to facilitate parental decision making regarding transition to palliative care. Copyright © 2015 Elsevier Inc. All rights reserved.

Studying a free fall experiment using short sequences of images

International Nuclear Information System (INIS)

Vera, Francisco; Romanque, Cristian

2008-01-01

We discuss a new alternative for obtaining position and time coordinates from a video of a free fall experiment. In our approach, after converting the video to a short sequence of images, the images are analyzed using a web page application developed by the author. The main advantage of the setup explained in this work, is that it is simple to use, no software license fees are necessary, and can be scaled-up to be used by a big number of students in introductory physics courses. The steps involved in the full analysis of a falling object are: we grab a short digital video of the experiment and convert it to a sequence of images, then, using a web page that includes all the necessary javascript, the student can easily click on the object of interest to obtain the (x,y,t) coordinates, finally, the student analyze motion using a spreadsheet.

Use of the Discrete Cosine Transform for the restoration of an image sequence

International Nuclear Information System (INIS)

Acheroy, M.P.J.

1985-01-01

The Discrete Cosine Transform (DCT) is recognized as an important tool for image compression techniques. Its use in image restoration is, however, not well known. It is the aim of this paper to provide a restoration method for a sequence of images using the DCT as well for the deblurring as for the noise reduction. It is shown that the DCT can play an interesting role in the deconvolution problem for linear imaging systems with finite, invariant and symmetric impulse response. It is further shown that the noise reduction can be performed onto an image sequence using a time adaptive Kalman filter in the domain of the Karhunen-Loeve transform which is approximated by the DCT

Comparison of single-shot fast spin-echo sequence and T2-weighted fast spin-echo sequence in MR imaging of the brain

International Nuclear Information System (INIS)

Cha, Sung Ho; Seo, Jeong Jin; Jeong, Gwang Woo; Kim, Jae Kyu; Kim, Yun Hyeon; Jeong, Yong Yeon; Kang, Heoung Keun; Oh, Hee Yeon; Yoon, Jong Hoon

1998-01-01

The purpose of this study was to evaluate the usefulness of the single-shot fast spinecho (SS-FSE) sequence in comparison with the T2-weighted fast spin-echo (T2-FSE) sequence in brain MR imaging. In 41 patients aged 15-75 years with intracranial lesion, both SS-FSE and T2-FES images were obtained using a 1.5-T MR system. Lesions included cerebral ischemia or infarcts (n=3D23), tumors (n=3D10), hemorrhages (n=3D3), inflammatory diseases (n=3D2), arachnoid cysts(n=3D2), and vascular disease (n=3D1), and the MR images were retrospectively evaluated. To calculate contrast-to-noise ratio (CNR), percentage contrast, and signal-to-noise ratio (SNR)-and thus make a quantitative comparison-the mean signal intensities of lesions, normal brain tissue, and noise out-side the patient were measured. For qualitative comparison, the visibility, margin, and extent of the lesions were rated using a five-grade system, and the degree of MR artifacts was also evaluated. Wilcoxon's signed ranks test was used for statistical analysis. The mean CNR of lesions was significantly higher on SS-FSE (31.3) than on T2-FSE images (27.5) (p=3D0.0131). Mean percentage contrast was also higher on SS-FSE (159.0) than on T2-FSE images (108.5) (p=3D0.0222), but mean SNR was higher on T2-FSE (80.3) than on SS-FSE images (53.5) (p=3D0.0000). No significant differences in lesion visibility were observed between the two imaging sequences, though margin and extent of the lesion were worse on SS-FSE images. For MR artifacts, no significant differences were demonstrated. For the evaluation of most intracranial lesions, MR imaging using the SS-FSE sequence appears to be slightly inferior to the T2-FSE sequence, but may be useful where patients are ill or uncooperative, or where children require sedation.=20

A novel method for fat suppression in RARE sequences

International Nuclear Information System (INIS)

Higuchi, Nobuya

1999-01-01

Rapid acquisition relaxation-enhanced (RARE) sequences utilize one or several Carr-Purcell-Meiboom-Gill (CPMG) echo trains to sample a number of k-space lines each repetition time TR. The technique can rapidly generate multislice T2-weighted images which, as a rule, are strikingly similar in contrast to conventional T2-weighted spin-echo (SE) images. An exception to this rule is the appearance of very bright signal from fat in T2-weighted RARE images as compared to conventional T2-weighted SE images. To reduce this fat signal, we introduce a time delay, τc, between the 90 degrees x and first 180 degrees y pulse of each echo train such that a phase angle of pi/2 develops between fat and the reference (water) line at echo maxima. The technique leads to single-acquisition fat suppression without the use of frequency-selective saturation pulses and concomitant loss of slices per TR. A Bloch equation analysis is used to identify two major mechanisms contributing to suppression of off-resonance spins such that w τc =pi/2. Namely, the CPMG sequence becomes a CP sequence with no self-correction properties for imperfect 180 degrees pulses leading to enhanced signal decay, and the raw k-space data matrix become segmented into blocks alternately multiplied by +/- i, leading to signal dispersion following Fourier transformation. (K.H.)

Gadolinium-Enhanced Three-Dimensional Magnetization - Prepared Rapid Gradient-Echo (3D MP-RAGE) Imaging is Superior to Spin-Echo Imaging in Delineating Brain Metastases

International Nuclear Information System (INIS)

Takeda, T.; Takeda, A.; Nagaoka, T.; Kunieda, E.; Takemasa, K.; Watanabe, M.; Hatou, T.; Oguro, S.; Katayama, M.

2008-01-01

Background: Precisely defining the number and location of brain metastases is very important for establishing a treatment strategy for malignancies. Although magnetic resonance imaging (MRI) is now considered the best modality, various improvements in sequences are still being made. Purpose: To prospectively compare the diagnostic ability of three-dimensional, magnetization-prepared rapid gradient-echo (3D MP-RAGE) imaging in detecting metastatic brain tumors, with that of two-dimensional spin-echo (2D SE) T1-weighted imaging. Material and Methods: A total of 123 examinations were included in this study, and 119 examinations from 88 patients with known malignancies were analyzed. All patients underwent T1- and T2-weighted 2D SE transverse imaging, followed by gadolinium-enhanced T1-weighted transverse and coronal 2D SE imaging and 3D MP-RAGE transverse imaging. Four radiologists interpreted the images to compare the accuracy and the time required for interpretation for each imaging. Results: 3D MP-RAGE imaging was significantly better than 2D SE imaging for detecting metastatic brain lesions, regardless of the readers' experience. The sensitivities of the 3D MP-RAGE and 2D SE imaging for all observers were 0.81 vs. 0.80 (P>0.05), specificities were 0.93 vs. 0.87 (P 0.05), and accuracies were 0.84 vs. 0.78 (P<0.05), respectively. There was no significant difference in the time required for image interpretation between the two modalities (15.6±4.0 vs. 15.4±4.1 min). Conclusion: 3D MP-RAGE imaging proved superior to 2D SE imaging in the detection of brain metastases

Pulse sequences and visualization of instruments

International Nuclear Information System (INIS)

Merkle, E.M.; Ulm Univ.; Wendt, M.; Chung, Y.C.; Duerk, J.L.; University Hospitals of Cleveland and Case Western Reserve University, OH; Lewin, J.S.

1998-01-01

While initially advocated primarily for intrasurgical visualization (e.g., craniotomy), interventional MRI rapidly evolved into roles in image-guided localization for needle-based procedures, minimally invasive neurosurgical procedures, and thermal ablation of cancer. In this contest, MRI pulse sequences and scanning methods serve one of four primary roles: (1) speed improvement, (2) device localization, (3) anatomy/lesion differentiation and (4) temperature sensitivity. The first part of this manuscript deals with passive visualization of MR-compatible needles and the effects of field strength, sequence design, and orientation of the needle relative to the static magnetic field of the scanner. Issues and recommendations are given for low-field as well as high-field scanners. The second part contains methods reported to achieve improved acquisition efficiency over conventional phase encoding (wavelets, locally focused imaging, singular value decomposition and keyhole imaging). Finally, the last part of the manuscrpt reports the current status of thermosensitive sequences and their dependence on spinlattice relaxation time (T1), water diffusion coefficient (D) and proton chemical shift (δ). (orig.) [de

Direct typing of Canine parvovirus (CPV) from infected dog faeces by rapid mini sequencing technique.

Science.gov (United States)

V, Pavana Jyothi; S, Akila; Selvan, Malini K; Naidu, Hariprasad; Raghunathan, Shwethaa; Kota, Sathish; Sundaram, R C Raja; Rana, Samir Kumar; Raj, G Dhinakar; Srinivasan, V A; Mohana Subramanian, B

2016-12-01

Canine parvovirus (CPV) is a non-enveloped single stranded DNA virus with an icosahedral capsid. Mini-sequencing based CPV typing was developed earlier to detect and differentiate all the CPV types and FPV in a single reaction. This technique was further evaluated in the present study by performing the mini-sequencing directly from fecal samples which avoided tedious virus isolation steps by cell culture system. Fecal swab samples were collected from 84 dogs with enteritis symptoms, suggestive of parvoviral infection from different locations across India. Seventy six of these samples were positive by PCR; the subsequent mini-sequencing reaction typed 74 of them as type 2a virus, and 2 samples as type 2b. Additionally, 25 of the positive samples were typed by cycle sequencing of PCR products. Direct CPV typing from fecal samples using mini-sequencing showed 100% correlation with CPV typing by cycle sequencing. Moreover, CPV typing was achieved by mini-sequencing even with faintly positive PCR amplicons which was not possible by cycle sequencing. Therefore, the mini-sequencing technique is recommended for regular epidemiological follow up of CPV types, since the technique is rapid, highly sensitive and high capacity method for CPV typing. Copyright © 2016. Published by Elsevier B.V.

Diuretic-enhanced gadolinium excretory MR urography: comparison of conventional gradient-echo sequences and echo-planar imaging

Energy Technology Data Exchange (ETDEWEB)

Nolte-Ernsting, C.C.A.; Tacke, J.; Adam, G.B.; Haage, P.; Guenther, R.W. [Univ. of Technology, Aachen (Germany). Dept. of Diagnostic Radiology; Jung, P.; Jakse, G. [Univ. of Technology, Aachen (Germany). Dept. of Urology

2001-01-01

The aim of this study was to investigate the utility of different gadolinium-enhanced T1-weighted gradient-echo techniques in excretory MR urography. In 74 urologic patients, excretory MR urography was performed using various T1-weighted gradient-echo (GRE) sequences after injection of gadolinium-DTPA and low-dose furosemide. The examinations included conventional GRE sequences and echo-planar imaging (GRE EPI), both obtained with 3D data sets and 2D projection images. Breath-hold acquisition was used primarily. In 20 of 74 examinations, we compared breath-hold imaging with respiratory gating. Breath-hold imaging was significantly superior to respiratory gating for the visualization of pelvicaliceal systems, but not for the ureters. Complete MR urograms were obtained within 14-20 s using 3D GRE EPI sequences and in 20-30 s with conventional 3D GRE sequences. Ghost artefacts caused by ureteral peristalsis often occurred with conventional 3D GRE imaging and were almost completely suppressed in EPI sequences (p < 0.0001). Susceptibility effects were more pronounced on GRE EPI MR urograms and calculi measured 0.8-21.7% greater in diameter compared with conventional GRE sequences. Increased spatial resolution degraded the image quality only in GRE-EPI urograms. (orig.)

Rapid sequence divergence rates in the 5 prime regulatory regions of young Drosophila melanogaster duplicate gene pairs

Directory of Open Access Journals (Sweden)

Michael H. Kohn

2008-01-01

Full Text Available While it remains a matter of some debate, rapid sequence evolution of the coding sequences of duplicate genes is characteristic for early phases past duplication, but long established duplicates generally evolve under constraint, much like the rest of the coding genome. As for coding sequences, it may be possible to infer evolutionary rate, selection, and constraint via contrasts between duplicate gene divergence in the 5 prime regions and in the corresponding synonymous site divergence in the coding regions. Finding elevated rates for the 5 prime regions of duplicated genes, in addition to the coding regions, would enable statements regarding the early processes of duplicate gene evolution. Here, 1 kb of each of the 5 prime regulatory regions of Drosophila melanogaster duplicate gene pairs were mapped onto one another to isolate shared sequence blocks. Genetic distances within shared sequence blocks (d5’ were found to increase as a function of synonymous (dS, and to a lesser extend, amino-acid (dA site divergence between duplicates. The rate d5’/dS was found to rapidly decay from values > 1 in young duplicate pairs (dS 0.8. Such rapid rates of 5 prime evolution exceeding 1 (~neutral predominantly were found to occur in duplicate pairs with low amino-acid site divergence and that tended to be co-regulated when assayed on microarrays. Conceivably, functional redundancy and relaxation of selective constraint facilitates subsequent positive selection on the 5 prime regions of young duplicate genes. This might promote the evolution of new functions (neofunctionalization or division of labor among duplicate genes (subfunctionalization. In contrast, similar to the vast portion of the non-coding genome, the 5 prime regions of long-established gene duplicates appear to evolve under selective constraint, indicating that these long-established gene duplicates have assumed critical functions.

Mobile Image Ratiometry: A New Method for Instantaneous Analysis of Rapid Test Strips

OpenAIRE

Donald C. Cooper; Bryan Callahan; Phil Callahan; Lee Burnett

2012-01-01

Here we describe Mobile Image Ratiometry (MIR), a new method for the automated quantification of standardized rapid immunoassay strips using consumer-based mobile smartphone and tablet cameras. To demonstrate MIR we developed a standardized method using rapid immunotest strips directed against cocaine (COC) and its major metabolite, benzoylecgonine (BE). We performed image analysis of three brands of commercially available dye-conjugated anti-COC/BE antibody test strips in response to three d...

Multiparametric magnetic resonance imaging of the prostate: current concepts.

NARCIS (Netherlands)

Bittencourt, L.K.; Hausmann, D.; Sabaneeff, N.; Gasparetto, E.L.; Barentsz, J.O.

2014-01-01

Multiparametric MR (mpMR) imaging is rapidly evolving into the mainstay in prostate cancer (PCa) imaging. Generally, the examination consists of T2-weighted sequences, diffusion-weighted imaging (DWI), dynamic contrast-enhanced (DCE) evaluation, and less often proton MR spectroscopy imaging (MRSI).

Development of rapid methods for relaxation time mapping and motion estimation using magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Gilani, Syed Irtiza Ali

2008-09-15

Recent technological developments in the field of magnetic resonance imaging have resulted in advanced techniques that can reduce the total time to acquire images. For applications such as relaxation time mapping, which enables improved visualisation of in vivo structures, rapid imaging techniques are highly desirable. TAPIR is a Look- Locker-based sequence for high-resolution, multislice T{sub 1} relaxation time mapping. Despite the high accuracy and precision of TAPIR, an improvement in the k-space sampling trajectory is desired to acquire data in clinically acceptable times. In this thesis, a new trajectory, termed line-sharing, is introduced for TAPIR that can potentially reduce the acquisition time by 40 %. Additionally, the line-sharing method was compared with the GRAPPA parallel imaging method. These methods were employed to reconstruct time-point images from the data acquired on a 4T high-field MR research scanner. Multislice, multipoint in vivo results obtained using these methods are presented. Despite improvement in acquisition speed, through line-sharing, for example, motion remains a problem and artefact-free data cannot always be obtained. Therefore, in this thesis, a rapid technique is introduced to estimate in-plane motion. The presented technique is based on calculating the in-plane motion parameters, i.e., translation and rotation, by registering the low-resolution MR images. The rotation estimation method is based on the pseudo-polar FFT, where the Fourier domain is composed of frequencies that reside in an oversampled set of non-angularly, equispaced points. The essence of the method is that unlike other Fourier-based registration schemes, the employed approach does not require any interpolation to calculate the pseudo-polar FFT grid coordinates. Translation parameters are estimated by the phase correlation method. However, instead of two-dimensional analysis of the phase correlation matrix, a low complexity subspace identification of the phase

Development of rapid methods for relaxation time mapping and motion estimation using magnetic resonance imaging

International Nuclear Information System (INIS)

Gilani, Syed Irtiza Ali

2008-09-01

Recent technological developments in the field of magnetic resonance imaging have resulted in advanced techniques that can reduce the total time to acquire images. For applications such as relaxation time mapping, which enables improved visualisation of in vivo structures, rapid imaging techniques are highly desirable. TAPIR is a Look- Locker-based sequence for high-resolution, multislice T 1 relaxation time mapping. Despite the high accuracy and precision of TAPIR, an improvement in the k-space sampling trajectory is desired to acquire data in clinically acceptable times. In this thesis, a new trajectory, termed line-sharing, is introduced for TAPIR that can potentially reduce the acquisition time by 40 %. Additionally, the line-sharing method was compared with the GRAPPA parallel imaging method. These methods were employed to reconstruct time-point images from the data acquired on a 4T high-field MR research scanner. Multislice, multipoint in vivo results obtained using these methods are presented. Despite improvement in acquisition speed, through line-sharing, for example, motion remains a problem and artefact-free data cannot always be obtained. Therefore, in this thesis, a rapid technique is introduced to estimate in-plane motion. The presented technique is based on calculating the in-plane motion parameters, i.e., translation and rotation, by registering the low-resolution MR images. The rotation estimation method is based on the pseudo-polar FFT, where the Fourier domain is composed of frequencies that reside in an oversampled set of non-angularly, equispaced points. The essence of the method is that unlike other Fourier-based registration schemes, the employed approach does not require any interpolation to calculate the pseudo-polar FFT grid coordinates. Translation parameters are estimated by the phase correlation method. However, instead of two-dimensional analysis of the phase correlation matrix, a low complexity subspace identification of the phase

Abdominal MR imaging using a HASTE sequence : image comparison on the different echo times

International Nuclear Information System (INIS)

Park, Kwang Bo; Lee, Moon Gyu; Lim, Tae Hwan; Jeong, Yoong Ki; Ha, Hyun Kwon; Kim, Pyo Nyun; Auh, Yong Ho

1999-01-01

To determine the optimal parameters of abdominal HASTE imaging by means of a comparison of intermediate and long TE (echo time). We evaluated 30 consecutive patients who had undergone liver MR during a three-month period. Twelve patients were diagnosed as normal, four as having liver cirrhosis, and 14 were found to be suffering form hepatic hemangioma. On the basis of measured signal intensity of the liver, spleen, pancreas and gallbladder, and of fat, muscle, hemangioma, and background, we calculated the ratios of signal to noise (S/N), signal difference to noise (SD/N), and signal intensity (SI). Image quality was compared using these three ratios, and using two HASTE sequences with TEs of 90 msec and 134 msec, images were qualitatively evaluated. S/N ratio of the liver was higher when TE was 90 msec(p<.05), though S/N, SD/N and SI rations of the spleen, gallbladder, and pancreas-and of hemangiom-were higher when TE was 134 msec (p<.05). However, in muscle, all these three ratios were higher at a TE of 90 msec. SD/N ratio and SI of fat were higher at a TE of 134 msec. Overall image quality was better at a TE of 134 msec than at one of 90msec. A HASTE sequence with a TE of 134msec showed greater tissue contrast and stronger T2-weighted images than one with a TE of 90msec

Estimation of physiological parameters using knowledge-based factor analysis of dynamic nuclear medicine image sequences

International Nuclear Information System (INIS)

Yap, J.T.; Chen, C.T.; Cooper, M.

1995-01-01

The authors have previously developed a knowledge-based method of factor analysis to analyze dynamic nuclear medicine image sequences. In this paper, the authors analyze dynamic PET cerebral glucose metabolism and neuroreceptor binding studies. These methods have shown the ability to reduce the dimensionality of the data, enhance the image quality of the sequence, and generate meaningful functional images and their corresponding physiological time functions. The new information produced by the factor analysis has now been used to improve the estimation of various physiological parameters. A principal component analysis (PCA) is first performed to identify statistically significant temporal variations and remove the uncorrelated variations (noise) due to Poisson counting statistics. The statistically significant principal components are then used to reconstruct a noise-reduced image sequence as well as provide an initial solution for the factor analysis. Prior knowledge such as the compartmental models or the requirement of positivity and simple structure can be used to constrain the analysis. These constraints are used to rotate the factors to the most physically and physiologically realistic solution. The final result is a small number of time functions (factors) representing the underlying physiological processes and their associated weighting images representing the spatial localization of these functions. Estimation of physiological parameters can then be performed using the noise-reduced image sequence generated from the statistically significant PCs and/or the final factor images and time functions. These results are compared to the parameter estimation using standard methods and the original raw image sequences. Graphical analysis was performed at the pixel level to generate comparable parametric images of the slope and intercept (influx constant and distribution volume)

First results in rapid MR imaging of focal liver and spleen lesions using field echos and small angle excitation (gradient echo sequences)

International Nuclear Information System (INIS)

Griebel, J.; Hess, C.F.; Kurtz, B.; Klose, U.; Kueper, K.

1987-01-01

15 healthy subjects and 39 patients with focal liver and spleen lesions were examined via MR tomography at 1.5 tesla. Gradient field echos at small angle excitation ( 0 ) were employed. The imaging time per layer was 10 seconds so that rapid imaging could be carried out at respiratory standstill. This enabled visualisation of liver and spleen without interference by breathing artifacts and with accurate localisation. Focal lesions can be imaged best at low flip-angle pulses (liver) or low to medium-angle pulses (spleen). The primary liver cell carcinoma is visualised as an inhomogeneous structure with similar signal intensity as the surrounding tissue. All other examined liver lesions (metastases, haemangiomas, lymphatic infiltrates, echinococcus cysts, FNH, gummae) showed greater signal intensity than the remaining organ at small angle excitation. Furthermore, contrast reversals were seen at medium-angle pulses. Contrariwise, with the exception of the light-coloured spleen infarcts, spleen lesions (lymphatic infiltrate, Boeck's disease or sarcoidosis) appeared darker at all excitation angles than the surrounding tissue. (orig.) [de

First results in rapid MR imaging of focal liver and spleen lesions using field echos and small angle excitation (gradient echo sequences)

Energy Technology Data Exchange (ETDEWEB)

Griebel, J.; Hess, C.F.; Kurtz, B.; Klose, U.; Kueper, K.

1987-01-01

15 healthy subjects and 39 patients with focal liver and spleen lesions were examined via MR tomography at 1.5 tesla. Gradient field echos at small angle excitation (< 90/sup 0/) were employed. The imaging time per layer was 10 seconds so that rapid imaging could be carried out at respiratory standstill. This enabled visualisation of liver and spleen without interference by breathing artifacts and with accurate localisation. Focal lesions can be imaged best at low flip-angle pulses (liver) or low to medium-angle pulses (spleen). The primary liver cell carcinoma is visualised as an inhomogeneous structure with similar signal intensity as the surrounding tissue. All other examined liver lesions (metastases, haemangiomas, lymphatic infiltrates, echinococcus cysts, FNH, gummae) showed greater signal intensity than the remaining organ at small angle excitation. Furthermore, contrast reversals were seen at medium-angle pulses. Contrariwise, with the exception of the light-coloured spleen infarcts, spleen lesions (lymphatic infiltrate, Boeck's disease or sarcoidosis) appeared darker at all excitation angles than the surrounding tissue.

Comparison of plastic single-use and metal reusable laryngoscope blades for orotracheal intubation during rapid sequence induction of anesthesia.

Science.gov (United States)

Amour, Julien; Marmion, Frédéric; Birenbaum, Aurélie; Nicolas-Robin, Armelle; Coriat, Pierre; Riou, Bruno; Langeron, Olivier

2006-01-01

Plastic single-use laryngoscope blades are inexpensive and carry a lower risk of infection compared with metal reusable blades, but their efficiency during rapid sequence induction remains a matter of debate. The authors therefore compared plastic and metal blades during rapid sequence induction in a prospective randomized trial. Two hundred eighty-four adult patients undergoing general anesthesia requiring rapid sequence induction were randomly assigned on a weekly basis to either plastic single-use or reusable metal blades (cluster randomization). After induction, a 60-s period was allowed to complete intubation. In the case of failed intubation, a second attempt was performed using metal blade. The primary endpoint of the study was the rate of failed intubations, and the secondary endpoint was the incidence of complications (oxygen desaturation, lung aspiration, and oropharynx trauma). Both groups were similar in their main characteristics, including risk factors for difficult intubation. On the first attempt, the rate of failed intubation was significantly increased in plastic blade group (17 vs. 3%; P < 0.01). In metal blade group, 50% of failed intubations were still difficult after the second attempt. In plastic blade group, all initial failed intubations were successfully intubated using metal blade, with an improvement in Cormack and Lehane grade. There was a significant increase in the complication rate in plastic group (15 vs. 6%; P < 0.05). In rapid sequence induction of anesthesia, the plastic laryngoscope blade is less efficient than a metal blade and thus should not be recommended for use in this clinical setting.

Inter frame motion estimation and its application to image sequence compression: an introduction

International Nuclear Information System (INIS)

Cremy, C.

1996-01-01

With the constant development of new communication technologies like, digital TV, teleconference, and the development of image analysis applications, there is a growing volume of data to manage. Compression techniques are required for the transmission and storage of these data. Dealing with original images would require the use of expansive high bandwidth communication devices and huge storage media. Image sequence compression can be achieved by means of interframe estimation that consists in retrieving redundant information relative to zones where there is little motion between two frames. This paper is an introduction to some motion estimation techniques like gradient techniques, pel-recursive, block-matching, and its application to image sequence compression. (Author) 17 refs

MR of normal pancreas : comparison of five pulse sequences and enhancing patterns on dynamic imaging

International Nuclear Information System (INIS)

Jang, Hyun Jung; Kim, Tae Kyoung; Hong, Sung Hwan; Han, Joon Koo; Choi, Byung Ihn

1997-01-01

To compare T1-weighted FLASH and turbo spin echo (SE) T2-weighted sequences with conventional T1- and T2-weighted sequences in imaging normal pancreas and to describe the enhancing patterns on dynamic MR imging. Forty-four patients with presumed hepatic hemangiomas were studied at 1.0T or 1.5T by using conventional SE sequences (T1-weighted, T2-weighted, and heavily T2-weighted), turbo-SE T2-weighted sequences, and breath-hold T1-weighted FLASH sequences acquired before, immediately on, and at 1, 2, 3, and 5 or 10 minutes after injection of a bolus of gadopentetate dimeglumine. No patients had either a history or its clinical features of pancreatic disease. Images were quantitatively analyzed for signal-difference-to noise ratios (SD/Ns) between the pancreas and peripancreatic fat. Percentage enhancement of the pancreas was measured on each dynamic MR image. Conspicuity of the pancreatic border was qualitatively evaluated according to a consensus, reached by three radiologists. Turbo-SE T2-weighted images had a significantly higher SD/N ratio (p<0.001) and better conspicuity of the pancreatic border (p<0.001) than SE T2- and heavily T2-weighted images;T1-weighted SE images had a significantly higher SD/N ratio than T1-weighted FLASH images (p<0.001), but there was no significant difference between tham in qualitative analysis (p=0.346). Percentage enhancement immediately on and at 1, 2, 3, 5, and 10 minutes after administration of contrast material was 39.9%, 44.5%, 42.9%, 40.8%, 36.3%, 29.9%, respectively, with peak enhancement at 1 minute. In MR imaging of normal pancreas, turbo-SE T2-weighted imaging is superior to SE T2- and heavily T2- weighted imaging, and SE T1-weighted imaging is superior to T1-weighted FLASH imaging. On serial gadolinium-enhanced FLASH imaging, normal pancreas shows peak enhancement at 1 minute

SPIO-enhanced MR imaging for HCC detection in cirrhotic patient : comparison of various techniques for optimal sequence selection

International Nuclear Information System (INIS)

Kim, In Hwan; Lee, Jeong Min; Kwak, Hyo Sung; Kim, Chong Soo; Yu, Hee Chul; Kim, Tae Kon; Lee Soo Tiek

2000-01-01

To compare the efficacy of breathhold and non-breathhold sequences in the detection of hepatocellular carcinoma (HCC) in cirrhotic patients using superparamagnetic iron oxide (SPIO)-enhanced MR imaging, and to determine the optimal sequence combination. By means of unenhanced and iron-oxide-enhanced MRI, 29 patients with 49 nodular HCCs were evaluated for the presence of HCC nodules. Twenty-one were male and eight were female, and their ages ranged from 38 to 71 (mean, 56) years. Eight different MR sequences were used, including four non-breath-hold sequences and four breath-hold, and images were obtained before and after the administration of SPIO particles. Non-breath-hold sequences included T2-, proton density-weighted SE, and TSE imaging, while breath-hold sequences comprised T1-weighted fast low-angle shot (T1w FLASH), half-Fourier acquisition single shot turbo spine echo (HASTE), T2-weighted fast imaging with steady-state free precession (T2 * wFISP) and T2-weighted breath-hold TSE (T2wBHTSE). Image analysis involved both quantitative and qualitative analysis. The quantitative parameters calculated were signal-to noise (S/N) ratios for livers and tumors, contrast to noise (C/N) ratios for tumors seen on precontrast and postcontrast images, and percentage of signal intensity loss (PSIL) after SPIO injection. Images were analysed qualitatively in terms of image artifacts and lesion conspicuity, and prior to calculating sensitivity, the number of lesions detected using various pulse sequences were counted. SPIO had a marked effect on liver S/N ratio but a minimal effect on tumor S/N ratio. PSIL was best in T2 * wFISP images, while T2wSE images showed the second-best results (p less than 0.05). Tumor-to-liver C/N values were also highest with T2 * wFISP, while T2wTSE and HASTE images were next. Qualitative study showed that non-breath hold images and FISP were better than breath hold images in terms of lesion conspicuity. The latter, however, were much better

The role of the STIR sequence in magnetic resonance imaging examination of bone tumours

International Nuclear Information System (INIS)

Golfieri, R.; Baddeley, H.; Pringle, J.S.; Souhami, R.

1990-01-01

Sixty patients with primary bone tumours were evaluated with magnetic resonance imaging (MRI) at 0.5 T with both conventional spin-echo (SE) and short inversion time inversion recovery (STIR) sequences. The STIR sequence with T 1 of 120-130 ms in all cases suppressed the high signal from fatty bone marrow, giving a clear depiction of tumour extent, in both its intramedullary and soft-tissue components, and is superior to conventional SE images. The high sensitivity (100% of our cases) of this technique is counterbalanced by its lack of specificity: on STIR sequences both tumour and peritumorous oedema give an increase of signal intensity, limiting assessment of tumour extent. Peritumoral oedema, only present in this series in malignant neoplasms, may however be differentiated on the basis of the configuration of the abnormal areas, and by comparing STIR images with short repetition time/echo time sequence results. (author)

Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

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Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

2017-10-01

Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Prehospital rapid sequence intubation improves functional outcome for patients with severe traumatic brain injury: a randomized controlled trial.

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Bernard, Stephen A; Nguyen, Vina; Cameron, Peter; Masci, Kevin; Fitzgerald, Mark; Cooper, David J; Walker, Tony; Std, B Paramed; Myles, Paul; Murray, Lynne; David; Taylor; Smith, Karen; Patrick, Ian; Edington, John; Bacon, Andrew; Rosenfeld, Jeffrey V; Judson, Rodney

2010-12-01

To determine whether paramedic rapid sequence intubation in patients with severe traumatic brain injury (TBI) improves neurologic outcomes at 6 months compared with intubation in the hospital. Severe TBI is associated with a high rate of mortality and long-term morbidity. Comatose patients with TBI routinely undergo endo-tracheal intubation to protect the airway, prevent hypoxia, and control ventilation. In many places, paramedics perform intubation prior to hospital arrival. However, it is unknown whether this approach improves outcomes. In a prospective, randomized, controlled trial, we assigned adults with severe TBI in an urban setting to either prehospital rapid sequence intubation by paramedics or transport to a hospital emergency department for intubation by physicians. The primary outcome measure was the median extended Glasgow Outcome Scale (GOSe) score at 6 months. Secondary end-points were favorable versus unfavorable outcome at 6 months, length of intensive care and hospital stay, and survival to hospital discharge. A total of 312 patients with severe TBI were randomly assigned to paramedic rapid sequence intubation or hospital intubation. The success rate for paramedic intubation was 97%. At 6 months, the median GOSe score was 5 (interquartile range, 1-6) in patients intubated by paramedics compared with 3 (interquartile range, 1-6) in the patients intubated at hospital (P = 0.28).The proportion of patients with favorable outcome (GOSe, 5-8) was 80 of 157 patients (51%) in the paramedic intubation group compared with 56 of 142 patients (39%) in the hospital intubation group (risk ratio, 1.28; 95% confidence interval, 1.00-1.64; P = 0.046). There were no differences in intensive care or hospital length of stay, or in survival to hospital discharge. In adults with severe TBI, prehospital rapid sequence intubation by paramedics increases the rate of favorable neurologic outcome at 6 months compared with intubation in the hospital.

Comprehensive MR imaging of acute gynecologic diseases.

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Dohke, M; Watanabe, Y; Okumura, A; Amoh, Y; Hayashi, T; Yoshizako, T; Yasui, M; Nakashita, S; Nakanishi, J; Dodo, Y

2000-01-01

Rapid advances in techniques of magnetic resonance (MR) imaging have enabled diagnosis of acute gynecologic conditions, which are characterized by sudden onset of lower abdominal pain, fever, genital bleeding, intraperitoneal bleeding, or symptoms of shock. The chemical-selective fat-suppression technique not only helps establish the characteristics of lesions that contain fat components but also increases the conspicuity of inflammatory lesions. When a T2-weighted image is obtained with a very long effective echo time (>250 msec), even a small amount of ascites can be easily identified and the contrast between urine and complex fluid becomes more conspicuous. T2*-weighted images are useful for identification of hemorrhagic lesions by demonstrating deoxyhemoglobin and hemosiderin. Contrast material-enhanced dynamic subtraction MR imaging performed with a three-dimensional fast field-echo sequence and a rapid bolus injection of gadopentetate dimeglumine allows evaluation of lesion vascularity and the anatomic relationship between pelvic vessels and a lesion and allows identification of the bleeding point by demonstrating extravasation of contrast material. To optimize the MR imaging examination, attention should be given to the parameters of each pulse sequence and proper combination of the sequences.

Imaging findings and referral outcomes of rapid assessment stroke clinics

International Nuclear Information System (INIS)

Widjaja, E.; Manuel, D.; Hodgson, T.J.; Connolly, D.J.A.; Coley, S.C.; Romanowski, C.A.J.; Gaines, P.; Cleveland, T.; Thomas, S.; Griffiths, P.D.; Doyle, C.; Venables, G.S.

2005-01-01

AIM: A rapid assessment stroke clinic (RASC) was established to provide a rapid diagnostic service to individuals with suspected transient cerebral or ocular ischaemia or recovered non-hospitalized strokes. In this report we review imaging findings and clinical outcomes of patients proceeding to the carotid surgery programme. METHODS: Between October 2000 and December 2002, 1339 people attended the RASC. The findings of head CT and carotid Doppler ultrasound of the 1320 patients who underwent brain and carotid imaging were reviewed, and the number subsequently proceeding to carotid angiography and intervention was reported. RESULTS: CT head scans were normal in 57% of cases; 38% demonstrated ischaemia or infarction; and 3% yielded incidental or other significant findings not related to ischaemia. On screening with carotid Doppler ultrasound, 7.5% showed greater than 50% stenosis on the symptomatic side. A total of 83 patients (6.2%) proceeded to cerebral angiography and 65 (4.8%) underwent carotid endarterectomy or endovascular repair. CONCLUSION: Rapid-access neurovascular clinics are efficient in selecting patients for carotid intervention, but this is at a cost and the number of potential strokes prevented is small. Alternative management pathways based on immediate medical treatment need to be evaluated

Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation

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Pleiner, Tino; Bates, Mark; Trakhanov, Sergei; Lee, Chung-Tien; Schliep, Jan Erik; Chug, Hema; Böhning, Marc; Stark, Holger; Urlaub, Henning; Görlich, Dirk

2015-01-01

Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target. DOI: http://dx.doi.org/10.7554/eLife.11349.001 PMID:26633879

Placental fetal stem segmentation in a sequence of histology images

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Athavale, Prashant; Vese, Luminita A.

2012-02-01

Recent research in perinatal pathology argues that analyzing properties of the placenta may reveal important information on how certain diseases progress. One important property is the structure of the placental fetal stems. Analysis of the fetal stems in a placenta could be useful in the study and diagnosis of some diseases like autism. To study the fetal stem structure effectively, we need to automatically and accurately track fetal stems through a sequence of digitized hematoxylin and eosin (H&E) stained histology slides. There are many problems in successfully achieving this goal. A few of the problems are: large size of images, misalignment of the consecutive H&E slides, unpredictable inaccuracies of manual tracing, very complicated texture patterns of various tissue types without clear characteristics, just to name a few. In this paper we propose a novel algorithm to achieve automatic tracing of the fetal stem in a sequence of H&E images, based on an inaccurate manual segmentation of a fetal stem in one of the images. This algorithm combines global affine registration, local non-affine registration and a novel 'dynamic' version of the active contours model without edges. We first use global affine image registration of all the images based on displacement, scaling and rotation. This gives us approximate location of the corresponding fetal stem in the image that needs to be traced. We then use the affine registration algorithm "locally" near this location. At this point, we use a fast non-affine registration based on L2-similarity measure and diffusion regularization to get a better location of the fetal stem. Finally, we have to take into account inaccuracies in the initial tracing. This is achieved through a novel dynamic version of the active contours model without edges where the coefficients of the fitting terms are computed iteratively to ensure that we obtain a unique stem in the segmentation. The segmentation thus obtained can then be used as an

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

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Patel Viren

2010-09-01

Full Text Available Abstract Background The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research. Results SeqAnt (Sequence Annotator is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds. Conclusion SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.

Rapid detection and purification of sequence specific DNA binding proteins using magnetic separation

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TIJANA SAVIC

2006-02-01

Full Text Available In this paper, a method for the rapid identification and purification of sequence specific DNA binding proteins based on magnetic separation is presented. This method was applied to confirm the binding of the human recombinant USF1 protein to its putative binding site (E-box within the human SOX3 protomer. It has been shown that biotinylated DNA attached to streptavidin magnetic particles specifically binds the USF1 protein in the presence of competitor DNA. It has also been demonstrated that the protein could be successfully eluted from the beads, in high yield and with restored DNA binding activity. The advantage of these procedures is that they could be applied for the identification and purification of any high-affinity sequence-specific DNA binding protein with only minor modifications.

Rapid, low-cost, image analysis through video processing

International Nuclear Information System (INIS)

Levinson, R.A.; Marrs, R.W.; Grantham, D.G.

1976-01-01

Remote Sensing now provides the data necessary to solve many resource problems. However, many of the complex image processing and analysis functions used in analysis of remotely-sensed data are accomplished using sophisticated image analysis equipment. High cost of this equipment places many of these techniques beyond the means of most users. A new, more economical, video system capable of performing complex image analysis has now been developed. This report describes the functions, components, and operation of that system. Processing capability of the new video image analysis system includes many of the tasks previously accomplished with optical projectors and digital computers. Video capabilities include: color separation, color addition/subtraction, contrast stretch, dark level adjustment, density analysis, edge enhancement, scale matching, image mixing (addition and subtraction), image ratioing, and construction of false-color composite images. Rapid input of non-digital image data, instantaneous processing and display, relatively low initial cost, and low operating cost gives the video system a competitive advantage over digital equipment. Complex pre-processing, pattern recognition, and statistical analyses must still be handled through digital computer systems. The video system at the University of Wyoming has undergone extensive testing, comparison to other systems, and has been used successfully in practical applications ranging from analysis of x-rays and thin sections to production of color composite ratios of multispectral imagery. Potential applications are discussed including uranium exploration, petroleum exploration, tectonic studies, geologic mapping, hydrology sedimentology and petrography, anthropology, and studies on vegetation and wildlife habitat

Direct sequencing for rapid detection of multidrug resistant Mycobacterium tuberculosis strains in Morocco.

Science.gov (United States)

Zakham, Fathiah; Chaoui, Imane; Echchaoui, Amina Hadbae; Chetioui, Fouad; Elmessaoudi, My Driss; Ennaji, My Mustapha; Abid, Mohammed; Mzibri, Mohammed El

2013-01-01

Tuberculosis (TB) is a major public health problem with high mortality and morbidity rates, especially in low-income countries. Disturbingly, the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) TB cases has worsened the situation, raising concerns of a future epidemic of virtually untreatable TB. Indeed, the rapid diagnosis of MDR TB is a critical issue for TB management. This study is an attempt to establish a rapid diagnosis of MDR TB by sequencing the target fragments of the rpoB gene which linked to resistance against rifampicin and the katG gene and inhA promoter region, which are associated with resistance to isoniazid. For this purpose, 133 sputum samples of TB patients from Morocco were enrolled in this study. One hundred samples were collected from new cases, and the remaining 33 were from previously treated patients (drug relapse or failure, chronic cases) and did not respond to anti-TB drugs after a sufficient duration of treatment. All samples were subjected to rpoB, katG and pinhA mutation analysis by polymerase chain reaction and DNA sequencing. Molecular analysis showed that seven strains were isoniazid-monoresistant and 17 were rifampicin-monoresistant. MDR TB strains were identified in nine cases (6.8%). Among them, eight were traditionally diagnosed as critical cases, comprising four chronic and four drug-relapse cases. The last strain was isolated from a new case. The most recorded mutation in the rpoB gene was the substitution TCG > TTG at codon 531 (Ser531 Leu), accounting for 46.15%. Significantly, the only mutation found in the katG gene was at codon 315 (AGC to ACC) with a Ser315Thr amino acid change. Only one sample harbored mutation in the inhA promoter region and was a point mutation at the -15p position (C > T). The polymerase chain reaction sequencing approach is an accurate and rapid method for detection of drug-resistant TB in clinical specimens, and could be of great interest in the management of TB in

Extended -Regular Sequence for Automated Analysis of Microarray Images

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Jin Hee-Jeong

2006-01-01

Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

Design and Applications of Rapid Image Tile Producing Software Based on Mosaic Dataset

Science.gov (United States)

Zha, Z.; Huang, W.; Wang, C.; Tang, D.; Zhu, L.

2018-04-01

Map tile technology is widely used in web geographic information services. How to efficiently produce map tiles is key technology for rapid service of images on web. In this paper, a rapid producing software for image tile data based on mosaic dataset is designed, meanwhile, the flow of tile producing is given. Key technologies such as cluster processing, map representation, tile checking, tile conversion and compression in memory are discussed. Accomplished by software development and tested by actual image data, the results show that this software has a high degree of automation, would be able to effectively reducing the number of IO and improve the tile producing efficiency. Moreover, the manual operations would be reduced significantly.

DESIGN AND APPLICATIONS OF RAPID IMAGE TILE PRODUCING SOFTWARE BASED ON MOSAIC DATASET

Directory of Open Access Journals (Sweden)

Z. Zha

2018-04-01

Full Text Available Map tile technology is widely used in web geographic information services. How to efficiently produce map tiles is key technology for rapid service of images on web. In this paper, a rapid producing software for image tile data based on mosaic dataset is designed, meanwhile, the flow of tile producing is given. Key technologies such as cluster processing, map representation, tile checking, tile conversion and compression in memory are discussed. Accomplished by software development and tested by actual image data, the results show that this software has a high degree of automation, would be able to effectively reducing the number of IO and improve the tile producing efficiency. Moreover, the manual operations would be reduced significantly.

Rapid Measurement and Correction of Phase Errors from B0 Eddy Currents: Impact on Image Quality for Non-Cartesian Imaging

Science.gov (United States)

Brodsky, Ethan K.; Klaers, Jessica L.; Samsonov, Alexey A.; Kijowski, Richard; Block, Walter F.

2014-01-01

Non-Cartesian imaging sequences and navigational methods can be more sensitive to scanner imperfections that have little impact on conventional clinical sequences, an issue which has repeatedly complicated the commercialization of these techniques by frustrating transitions to multi-center evaluations. One such imperfection is phase errors caused by resonant frequency shifts from eddy currents induced in the cryostat by time-varying gradients, a phenomemon known as B0 eddy currents. These phase errors can have a substantial impact on sequences that use ramp sampling, bipolar gradients, and readouts at varying azimuthal angles. We present a method for measuring and correcting phase errors from B0 eddy currents and examine the results on two different scanner models. This technique yields significant improvements in image quality for high-resolution joint imaging on certain scanners. The results suggest that correction of short time B0 eddy currents in manufacturer provided service routines would simplify adoption of non-Cartesian sampling methods. PMID:22488532

Removing the bottleneck in whole genome sequencing of Mycobacterium tuberculosis for rapid drug resistance analysis: a call to action

Directory of Open Access Journals (Sweden)

Ruth McNerney

2017-03-01

Full Text Available Whole genome sequencing (WGS can provide a comprehensive analysis of Mycobacterium tuberculosis mutations that cause resistance to anti-tuberculosis drugs. With the deployment of bench-top sequencers and rapid analytical software, WGS is poised to become a useful tool to guide treatment. However, direct sequencing from clinical specimens to provide a full drug resistance profile remains a serious challenge. This article reviews current practices for extracting M. tuberculosis DNA and possible solutions for sampling sputum. Techniques under consideration include enzymatic digestion, physical disruption, chemical degradation, detergent solubilization, solvent extraction, ligand-coated magnetic beads, silica columns, and oligonucleotide pull-down baits. Selective amplification of genomic bacterial DNA in sputum prior to WGS may provide a solution, and differential lysis to reduce the levels of contaminating human DNA is also being explored. To remove this bottleneck and accelerate access to WGS for patients with suspected drug-resistant tuberculosis, it is suggested that a coordinated and collaborative approach be taken to more rapidly optimize, compare, and validate methodologies for sequencing from patient samples.

Object-Oriented Query Language For Events Detection From Images Sequences

Science.gov (United States)

Ganea, Ion Eugen

2015-09-01

In this paper is presented a method to represent the events extracted from images sequences and the query language used for events detection. Using an object oriented model the spatial and temporal relationships between salient objects and also between events are stored and queried. This works aims to unify the storing and querying phases for video events processing. The object oriented language syntax used for events processing allow the instantiation of the indexes classes in order to improve the accuracy of the query results. The experiments were performed on images sequences provided from sport domain and it shows the reliability and the robustness of the proposed language. To extend the language will be added a specific syntax for constructing the templates for abnormal events and for detection of the incidents as the final goal of the research.

Rapid, low dose X-ray diffractive imaging of the malaria parasite Plasmodium falciparum

International Nuclear Information System (INIS)

Jones, Michael W.M.; Dearnley, Megan K.; Riessen, Grant A. van; Abbey, Brian; Putkunz, Corey T.; Junker, Mark D.; Vine, David J.; McNulty, Ian; Nugent, Keith A.; Peele, Andrew G.; Tilley, Leann

2014-01-01

Phase-diverse X-ray coherent diffractive imaging (CDI) provides a route to high sensitivity and spatial resolution with moderate radiation dose. It also provides a robust solution to the well-known phase-problem, making on-line image reconstruction feasible. Here we apply phase-diverse CDI to a cellular sample, obtaining images of an erythrocyte infected by the sexual stage of the malaria parasite, Plasmodium falciparum, with a radiation dose significantly lower than the lowest dose previously reported for cellular imaging using CDI. The high sensitivity and resolution allow key biological features to be identified within intact cells, providing complementary information to optical and electron microscopy. This high throughput method could be used for fast tomographic imaging, or to generate multiple replicates in two-dimensions of hydrated biological systems without freezing or fixing. This work demonstrates that phase-diverse CDI is a valuable complementary imaging method for the biological sciences and ready for immediate application. - Highlights: • Phase-diverse coherent X-ray diffraction microscopy provides high-resolution and high-contrast images of intact biological samples. • Rapid nanoscale resolution imaging is demonstrated at orders of magnitude lower dose than previously possible. • Phase-diverse coherent X-ray diffraction microscopy is a robust technique for rapid, quantitative, and correlative X-ray phase imaging

Rapid, low dose X-ray diffractive imaging of the malaria parasite Plasmodium falciparum

Energy Technology Data Exchange (ETDEWEB)

Jones, Michael W.M., E-mail: michael.jones@latrobe.edu.au [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Dearnley, Megan K. [ARC Centre of Excellence for Coherent X-Ray Science, Department of Biochemistry and Molecular Biology, Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia); Riessen, Grant A. van [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Abbey, Brian [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Melbourne Centre for Nanofabrication, Victoria 3168 (Australia); Putkunz, Corey T. [ARC Centre of Excellence for Coherent X-Ray Science, School of Physics, The University of Melbourne, Victoria 3010 (Australia); Junker, Mark D. [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Vine, David J. [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); McNulty, Ian [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); Centre for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Nugent, Keith A. [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Peele, Andrew G. [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Australian Synchrotron, 800 Blackburn Road, Clayton 3168 (Australia); Tilley, Leann [ARC Centre of Excellence for Coherent X-Ray Science, Department of Biochemistry and Molecular Biology, Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia)

2014-08-01

Phase-diverse X-ray coherent diffractive imaging (CDI) provides a route to high sensitivity and spatial resolution with moderate radiation dose. It also provides a robust solution to the well-known phase-problem, making on-line image reconstruction feasible. Here we apply phase-diverse CDI to a cellular sample, obtaining images of an erythrocyte infected by the sexual stage of the malaria parasite, Plasmodium falciparum, with a radiation dose significantly lower than the lowest dose previously reported for cellular imaging using CDI. The high sensitivity and resolution allow key biological features to be identified within intact cells, providing complementary information to optical and electron microscopy. This high throughput method could be used for fast tomographic imaging, or to generate multiple replicates in two-dimensions of hydrated biological systems without freezing or fixing. This work demonstrates that phase-diverse CDI is a valuable complementary imaging method for the biological sciences and ready for immediate application. - Highlights: • Phase-diverse coherent X-ray diffraction microscopy provides high-resolution and high-contrast images of intact biological samples. • Rapid nanoscale resolution imaging is demonstrated at orders of magnitude lower dose than previously possible. • Phase-diverse coherent X-ray diffraction microscopy is a robust technique for rapid, quantitative, and correlative X-ray phase imaging.

SU-E-J-216: A Sequence Independent Approach for Quantification of MR Image Deformations From Brachytherapy Applicators

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Wieringen, N van; Heerden, L van; Gurney-Champion, O; Kesteren, Z van; Houweling, A; Pieters, B; Bel, A [Academic Medical Center, Amsterdam (Netherlands)

2015-06-15

Purpose: MRI is increasingly used as a single imaging modality for brachytherapy treatment planning. The presence of a brachytherapy applicator may cause distortions in the images, especially at higher field strengths. Our aim is to develop a procedure to quantify these distortions theoretically for any MR-sequence and to verify the estimated deformations for clinical sequences. Methods: Image distortions due to perturbation of the B0-field are proportional to the ratio of the induced frequency shift and the read-out bandwidth of the applied sequence. By reconstructing a frequency-shift map from the phase data from a multi-echo sequence, distortions can be calculated for any MR-sequence. Verification of this method for estimating distortions was performed by acquiring images with opposing read-out directions and consequently opposing distortions. The applicator shift can be determined by rigidly matching these images. Clinically, T2W-TSE-images are used for this purpose. For pre-clinical tests, EPI-sequences with narrow read-out bandwidth (19.5–47.5Hz), consequently large distortions, were added to the set of clinical MRsequences. To quantify deformations of the Utrecht Interstitial CT/MR applicator (Elekta Brachytherapy) on a Philips Ingenia 3T MRI, pre-clinical tests were performed in a phantom with the applicator in water, followed by clinical validation. Results: Deformations observed in the narrow bandwidth EPI-images were well predicted using the frequency-shift, the latter giving an overestimation up to 30%/up to 1 voxel. For clinically applied MR-sequences distortions were well below the voxel size. In patient setup distortions determined from the frequency-shift map were at sub-voxel level (<0.7mm). Using T2W-images larger distortions were found (1–2mm). This discrepancy was caused by patient movement between/during acquisition of the T2W-images with opposing read-out directions. Conclusion: Phantom experiments demonstrated the feasibility of a

Fast spin-echo imaging

International Nuclear Information System (INIS)

Mackey, K.; Zoarski, G.; Bentson, J.R.; Lufkin, R.B.; Melki, P.; Jolesz, F.

1991-01-01

This paper reports on a partial radio-frequency (RF) echo-planar pulse sequence called contiguous slice fast spin echo (CSFSE) which is undergoing clinical trials for spine MR imaging. In this variation of rapid acquisition relaxation enhanced (RARE) spin-echo imaging, rapid 180 degrees RF pulse generated refocused echoes, producing T2-weighted images in about one-third the time of conventional double-echo technique. Forty patients with suspected pathology of the spine were imaged with conventional double-echo and closely matched CSFSE techniques on a GE Signa 1.5-T Advantage system. Cases were reviewed by two board-certified neuroradiologists. In all cases the CSFSE images were of equal or superior quality compared with those obtained with the conventional double-echo technique. Pathologic processes that were imaged consisted of inflammatory, neoplastic, posttraumatic, and degenerative conditions

Selection of optimal pulse sequences for conventional and dynamic MR imaging with Gd-DTPA; A fundamental study

Energy Technology Data Exchange (ETDEWEB)

Maeda, Miho; Kita, Keisuke; Maeda, Masayuki (Wakayama Medical Coll. (Japan)) (and others)

1989-11-01

Gadolinium-DTPA (Gd-DTPA) enhances contrast between tissues in magnetic resonance (MR) imaging. The enhancement of tissues depends partly upon the pulse sequences, and the optimal pulse sequence is also influenced by the tissue cncentration of Gd-DTPA. We prepared phantoms of 25% albumin solutions with various concentrations of Gd-DTPA, and imaged them using various pulse sequences with 1.5-T MR system. We also performed MR imaging of 16 patients with tumors (10 brain tumors and 6 hepatic tumors) before and after intravenous administration of Gd-DTPA (0.1 mmol/kg); 6 patients with hepatic tumors underwent dynamic MR imaging during suspended respiration. We made a theoretical equation to calculate the concentration of Gd-DTPA and estimated its tissue concentration in tumors at 0{approx}0.2 mmol/kg. Within these tissue concentrations, the enhancement-to-noise (E/N) ratio was larger in FISP (flip angle of 90deg, TR pf 300 msec, minimal TE) and SE (TR of 400 msec, minimal TE) sequences than in other sequences observed. These sequences may be preferable for conventional enhanced-MRI. Among the pulse sequences with TR of less than 100 msec, FISP (flip angle of 90deg, TR of less than 100 msec, minimal TE) had the largest E/N ratio; which may be useful for dynamic MRI during suspended respiration. The importance of selecting the optimal pulse sequences according to the imaging modality used will be discussed. (author).

MR imaging characteristics of intracranial hemorrhage using gradient-echo signal acquisition at 1.5 T: Comparison with spin-echo imaging and clinical applications

International Nuclear Information System (INIS)

Atlas, S.W.; Grossman, R.I.; Gomori, J.M.; Hackney, D.B.; Goldberg, H.I.; Bilaniuk, L.T.; Zimmerman, R.A.

1987-01-01

Evolving paramagnetic blood-breakdown products create static local magnetic susceptibility gradients, which induce rapid phase dispersion on the basis of T2/sup */ shortening. The authors evaluated 30 patients with 50 separate hemorrhagic intracranial lesions with both spin-echo (SE) and gradient echo signal acquisition (GESA) MR imaging at 1.5 T. GESA sequences used repetition time (TR) of 200-750 msec, echo time (TE) of 50-80 msec, and flip angles of 10 0 to 15 0 to emphasize T2/sup */-based contributions to contrast. SE sequences in all cases utilized both short and long TR (600 and 2,500-3,000 msec), with TE of 20-120 msec. Advantages of GESA imaging with Long TE and short flip angles in the evaluation of intracranial hemorrhage include (1) increased sensitivity to susceptibility-induced phase loss from T2/sup */ shortening, resulting in detection of hemorrhagic lesions not seen on conventional long TR/long TE SE images, and (2) very rapid acquisition of images with T2/sup */-based contrast. Limitations of this sequence include (1) severe diamagnetic susceptibility-induced artifacts, especially near air-brain interfaces, which often obscure large portions of the brain and occasionally simulate serious pathology, (2) characteristic internal signal intensity patterns demonstrated by SE imaging, such as in evolving hematomas, occult vascular malformations, and hemorrhagic malignancies, are often obscured by marked hypointensity on GESA images, and (3) reduced signal-noise ratio. The authors conclude that, although images with marked sensitivity to T2/sup */ effects can be rapidly generated by GESA, there is only a limited role for this sequence when evaluating intracranial hemorrhage at 1.5 T, and, in fact, significant information is lost when compared to SE images

Moving target detection based on temporal-spatial information fusion for infrared image sequences

Science.gov (United States)

Toing, Wu-qin; Xiong, Jin-yu; Zeng, An-jun; Wu, Xiao-ping; Xu, Hao-peng

2009-07-01

Moving target detection and localization is one of the most fundamental tasks in visual surveillance. In this paper, through analyzing the advantages and disadvantages of the traditional approaches about moving target detection, a novel approach based on temporal-spatial information fusion is proposed for moving target detection. The proposed method combines the spatial feature in single frame and the temporal properties within multiple frames of an image sequence of moving target. First, the method uses the spatial image segmentation for target separation from background and uses the local temporal variance for extracting targets and wiping off the trail artifact. Second, the logical "and" operator is used to fuse the temporal and spatial information. In the end, to the fusion image sequence, the morphological filtering and blob analysis are used to acquire exact moving target. The algorithm not only requires minimal computation and memory but also quickly adapts to the change of background and environment. Comparing with other methods, such as the KDE, the Mixture of K Gaussians, etc., the simulation results show the proposed method has better validity and higher adaptive for moving target detection, especially in infrared image sequences with complex illumination change, noise change, and so on.

[Factors of the rapid startup for nitrosation in sequencing batch reactor].

Science.gov (United States)

Li, Dong; Tao, Xiao-Xiao; Li, Zhan; Wang, Jun-An; Zhang, Jie

2011-08-01

The approach and factors for realizing the rapid startup of nitrosation were researched at the low level of dissolved oxygen (DO) in sequencing batch reactor (SBR). The main parameters of the reactor were controlled as follows: DO were 0.15-0.40 mg/L, pH values kept from 7.52 to 8.30, temperature maintained at 22.3-27.1 degrees C, and time of aeration was 8 hours. The purpose of rapid startup for nitrosation was achieved after 57 cycles (36 d) with the alternative influent of high and low ammonium wastewater (the mean values were 245.28 mg/L and 58.08 mg/L respectively) in a SBR, and the nitrosation rate was even 100%. Factors of accumulation of nitrite were investigated and the effects of DO and pH were analyzed during the startup for nitrosation. The results showed that it could improve the efficiency of nitrosation when DO concentration was increased appropriately. The activity of nitrite oxidizing bacteria (NOB) was recovered gradually when DO was higher than 0.72 mg/L. The key factor of controlling nitrosation reaction was the concentration of free ammonia (FA), while the final factor was the concentration of DO. pH was a desired controlling parameter to show the end of nitrification in a SBR cycle, while DO concentration did not indicate the finishing of SBR nitrification accurately because it increased rapidly before ammonia nitrogen was oxidized absolutely.

Magnetic resonance imaging of anterior cruciate ligament of the knee: a comparison of four sequences

International Nuclear Information System (INIS)

Casillas, C.; Marti-Bonmati, L.; Molla, E.; Ferrer, P.; Dosda, R.

1999-01-01

To compare the diagnostic efficacy of the four magnetic resonance imaging (MRI) sequences that compose the standard protocol for the study of the knee in our center when employed in the examination of anterior cruciate ligament (ACL). A prospective study was carried out based on MRI findings in the knees of 326 consecutive patients. Sagittal [proton density (PD w eighted turbo-spin-echo and T2*-weighted gradient echo], coronal (PD-weighted turbo-spin-echo with fat suppression) and transverse (T2*-weighted gradient echo with magnetization transfer) images were evaluated. Each sequence was analyzed independently by two radiologists, while another two assessed all the sequences together with the clinical findings. Four categories were established: normal ACL, partially torn, completely torn and synovialized. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) with respect to the definitive diagnosis were calculated for each sequence. The statistical analysis of the findings for each category was done using the chi-squared test and the Kappa test was employed to assess the degree of agreement. According to the final diagnosis, 263 ACL were normal, 29 were partially torn, 33 were completely torn and there was 1 case of synovialization associated with a completely torn ACL. The relationship between the analysis of the ACL according to each sequence and the definitive diagnosis was very significant (p<0.001) and the agreement was excellent. All the sequences presented similar levels of diagnostic precision. The coronal sequence had least number of diagnostic errors (2.1%). The combinations of imaging techniques that resulted in the lowest error rate with respect to the definitive diagnosis were coronal PD-weighted turbo-spin-echo with fat suppression and sagittal PD-weighted turbo-spin-echo. Coronal images are highly precise in the evaluation of ACL. Sagittal sequences are the most valid for diagnosis of torn ACL. Transverse

On the Farey sequence and its augmentation for applications to image analysis

Directory of Open Access Journals (Sweden)

Pratihar Sanjoy

2017-09-01

Full Text Available We introduce a novel concept of the augmented Farey table (AFT. Its purpose is to store the ranks of fractions of a Farey sequence in an efficient manner so as to return the rank of any query fraction in constant time. As a result, computations on the digital plane can be crafted down to simple integer operations; for example, the tasks like determining the extent of collinearity of integer points or of parallelism of straight lines—often required to solve many image-analytic problems—can be made fast and efficient through an appropriate AFT-based tool. We derive certain interesting characterizations of an AFT for its efficient generation. We also show how, for a fraction not present in a Farey sequence, the rank of the nearest fraction in that sequence can efficiently be obtained by the regula falsi method from the AFT concerned. To assert its merit, we show its use in two applications—one in polygonal approximation of digital curves and the other in skew correction of engineering drawings in document images. Experimental results indicate the potential of the AFT in such image-analytic applications.

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

Science.gov (United States)

Rowe, Will; Baker, Kate S; Verner-Jeffreys, David; Baker-Austin, Craig; Ryan, Jim J; Maskell, Duncan; Pearce, Gareth

2015-01-01

Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR

Retrospective comparison of three-dimensional imaging sequences in the visualization of posterior fossa cranial nerves.

Science.gov (United States)

Ors, Suna; Inci, Ercan; Turkay, Rustu; Kokurcan, Atilla; Hocaoglu, Elif

2017-12-01

To compare efficancy of three-dimentional SPACE (sampling perfection with application-optimized contrasts using different flip-angle evolutions) and CISS (constructive interference in steady state) sequences in the imaging of the cisternal segments of cranial nerves V-XII. Temporal MRI scans from 50 patients (F:M ratio, 27:23; mean age, 44.5±15.9 years) admitted to our hospital with vertigo, tinnitus, and hearing loss were retrospectively analyzed. All patients had both CISS and SPACE sequences. Quantitative analysis of SPACE and CISS sequences was performed by measuring the ventricle-to-parenchyma contrast-to-noise ratio (CNR). Qualitative analysis of differences in visualization capability, image quality, and severity of artifacts was also conducted. A score ranging 'no artefact' to 'severe artefacts and unreadable' was used for the assessment of artifacts and from 'not visualized' to 'completely visualized' for the assesment of image quality, respectively. The distribution of variables was controlled by the Kolmogorov-Smirnov test. Samples t-test and McNemar's test were used to determine statistical significance. Rates of visualization of posterior fossa cranial nerves in cases of complete visualization were as follows: nerve V (100% for both sequences), nerve VI (94% in SPACE, 86% in CISS sequences), nerves VII-VIII (100% for both sequences), IX-XI nerve complex (96%, 88%); nerve XII (58%, 46%) (p<0.05). SPACE sequences showed fewer artifacts than CISS sequences (p<0.002). Copyright © 2017 Elsevier B.V. All rights reserved.

Extracting a Good Quality Frontal Face Image from a Low-Resolution Video Sequence

DEFF Research Database (Denmark)

Nasrollahi, Kamal; Moeslund, Thomas B.

2011-01-01

Feeding low-resolution and low-quality images, from inexpensive surveillance cameras, to systems like, e.g., face recognition, produces erroneous and unstable results. Therefore, there is a need for a mechanism to bridge the gap between on one hand low-resolution and low-quality images......, we use a learning-based super-resolution algorithm applied to the result of the reconstruction-based part to improve the quality by another factor of two. This results in an improvement factor of four for the entire system. The proposed system has been tested on 122 low-resolution sequences from two...... different databases. The experimental results show that the proposed system can indeed produce a high-resolution and good quality frontal face image from low-resolution video sequences....

Rapid magnetic resonance imaging protocol for detecting femoral head avascular necrosis: A case series-it′s utility in the general population in developing countries

Directory of Open Access Journals (Sweden)

M Sanjay Khaladkar

2015-01-01

Full Text Available Introduction: Osteonecrosis of the femoral head is an increasing cause of musculoskeletal disability, common among the younger population, between the third and fifth decade of life, affecting mainly men, thereby requiring prompt diagnosis and early intervention. Aims and Objectives: The aim was to formulate a limited magnetic resonance imaging (MRI examination protocol for detection of avascular necrosis (AVN in clinically suspected cases that can be performed rapidly and will be inexpensive. Materials and Methods: Forty-five patients suspected clinically and or on conventional radiography for AVN of the femoral head were referred for MRI hip. MRI hip was done on 1.5 T Siemens Avanto. Of 45, 36 were detected to have AVN (total 58 hips, whereas 9 did not have AVN on MRI. Initially, coronal T1-weighted image (T1WI sequence was obtained as limited MRI protocol, followed by complete MRI examination. Results: Maximum patients belonged to age group 31-40 (30.5%. 32 (88.88% patients were males and 4 (11.11% were females. Bilateral AVN was detected in 44 (61.1% and unilateral in 14 patients (38.8%. Pre collapsed stage (Stages I and II was detected in 18 hips (31.03%, collapsed stage (Stages III and IV was detected in 40 hips (68.9%. Peripheral low-intensity rim was seen on T1WI in all 58 cases of AVN. Double line sign on T2-weighted image was seen in 33/58 (56.8%. Conclusion: Our study concluded that coronal T1W sequence is an easy, rapid and cost-effective method of detecting unilateral or bilateral AVN.

Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.

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Dario Cantu

Full Text Available BACKGROUND: The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130. METHODOLOGY/PRINCIPAL FINDINGS: We obtained nearly 80 million high quality paired-end reads (>50x coverage that were assembled into 29,178 contigs (64.8 Mb, which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase. CONCLUSIONS/SIGNIFICANCE: The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for

Rapid development of microsatellite markers for Callosobruchus chinensis using Illumina paired-end sequencing.

Directory of Open Access Journals (Sweden)

Can-Xing Duan

Full Text Available BACKGROUND: The adzuki bean weevil, Callosobruchus chinensis L., is one of the most destructive pests of stored legume seeds such as mungbean, cowpea, and adzuki bean, which usually cause considerable loss in the quantity and quality of stored seeds during transportation and storage. However, a lack of genetic information of this pest results in a series of genetic questions remain largely unknown, including population genetic structure, kinship, biotype abundance, and so on. Co-dominant microsatellite markers offer a great resolving power to determine these events. Here, we report rapid microsatellite isolation from C. chinensis via high-throughput sequencing. PRINCIPAL FINDINGS: In this study, 94,560,852 quality-filtered and trimmed reads were obtained for the assembly of genome using Illumina paired-end sequencing technology. In total, the genome with total length of 497,124,785 bp, comprising 403,113 high quality contigs was generated with de novo assembly. More than 6800 SSR loci were detected and a suit of 6303 primer pair sequences were designed and 500 of them were randomly selected for validation. Of these, 196 pair of primers, i.e. 39.2%, produced reproducible amplicons that were polymorphic among 8 C. chinensis genotypes collected from different geographical regions. Twenty out of 196 polymorphic SSR markers were used to analyze the genetic diversity of 18 C. chinensis populations. The results showed the twenty SSR loci were highly polymorphic among these populations. CONCLUSIONS: This study presents a first report of genome sequencing and de novo assembly for C. chinensis and demonstrates the feasibility of generating a large scale of sequence information and SSR loci isolation by Illumina paired-end sequencing. Our results provide a valuable resource for C. chinensis research. These novel markers are valuable for future genetic mapping, trait association, genetic structure and kinship among C. chinensis.

A survey of a population of anaesthesiologists from South India regarding practices for rapid sequence intubation in patients with head injury

Directory of Open Access Journals (Sweden)

Satyen Parida

2016-01-01

Full Text Available Background and Aims: Evidence and utility of the individual steps of the rapid sequence induction and tracheal intubation protocols have been debated, especially in the setting of traumatic brain injury. The purpose of this survey was to determine preferences in the current approach to rapid sequence intubation ( RSI in head injury patients among a population of anaesthesiologists from South India. Methods: A questionnaire was E-mailed to all the members of the Indian Society of Anaesthesiologists′ South Zone Chapter to ascertain their preferences, experience and comfort level with regard to their use of rapid sequence intubation techniques in adult patients with head injury. Participants were requested to indicate their practices for RSI technique for a head-injured patient upon arrival at the Emergency Medical Services department of their hospital. Results: The total response rate was 56.9% (530/932. Of the total respondents, 35% of the clinicians used cricoid pressure routinely, most respondents (68% stated that they pre-oxygenate the patients for about 3 min prior to RSI, thiopentone (61% and propofol (34% were commonly used prior to intubation. Rocuronium was the muscle relaxant of choice for RSI among the majority (44%, compared to succinylcholine (39%. Statistical analyses were performed after the initial entry onto a spreadsheet. Data were summarised descriptively using frequency distribution. Conclusion: In a rapid sequence intubation situation, the practice differed significantly among anaesthesiologists. Owing to disagreements and paucity of evidence-based data regarding the standards of RSI, it is apparent that RSI practice still has considerable variability in clinical practice.

TRDistiller: a rapid filter for enrichment of sequence datasets with proteins containing tandem repeats.

Science.gov (United States)

Richard, François D; Kajava, Andrey V

2014-06-01

The dramatic growth of sequencing data evokes an urgent need to improve bioinformatics tools for large-scale proteome analysis. Over the last two decades, the foremost efforts of computer scientists were devoted to proteins with aperiodic sequences having globular 3D structures. However, a large portion of proteins contain periodic sequences representing arrays of repeats that are directly adjacent to each other (so called tandem repeats or TRs). These proteins frequently fold into elongated fibrous structures carrying different fundamental functions. Algorithms specific to the analysis of these regions are urgently required since the conventional approaches developed for globular domains have had limited success when applied to the TR regions. The protein TRs are frequently not perfect, containing a number of mutations, and some of them cannot be easily identified. To detect such "hidden" repeats several algorithms have been developed. However, the most sensitive among them are time-consuming and, therefore, inappropriate for large scale proteome analysis. To speed up the TR detection we developed a rapid filter that is based on the comparison of composition and order of short strings in the adjacent sequence motifs. Tests show that our filter discards up to 22.5% of proteins which are known to be without TRs while keeping almost all (99.2%) TR-containing sequences. Thus, we are able to decrease the size of the initial sequence dataset enriching it with TR-containing proteins which allows a faster subsequent TR detection by other methods. The program is available upon request. Copyright © 2014 Elsevier Inc. All rights reserved.

Pictorial review: magnetic resonance imaging of colonic diverticulitis

International Nuclear Information System (INIS)

Buckley, Orla; Geoghegan, Tony; McAuley, Grainne; Persaud, Thara; Khosa, Faisal; Torreggiani, William C.

2007-01-01

Magnetic resonance imaging (MRI) is rapidly emerging as a useful imaging modality for the evaluation of the gastrointestinal tract. Increasingly rapid sequences and improving hardware have significantly improved the visualisation of diseases of the colon. MRI has a major advantage over CT in that there is no ionising radiation. In our institution, MRI has increasingly been used as a complimentary imaging modality to CT in the diagnosis and evaluation of diverticulitis and its complications. In this review article, we illustrate the emerging role of MRI in the diagnosis and evaluation of colonic diverticulitis. (orig.)

Motion Analysis Based on Invertible Rapid Transform

Directory of Open Access Journals (Sweden)

J. Turan

1999-06-01

Full Text Available This paper presents the results of a study on the use of invertible rapid transform (IRT for the motion estimation in a sequence of images. Motion estimation algorithms based on the analysis of the matrix of states (produced in the IRT calculation are described. The new method was used experimentally to estimate crowd and traffic motion from the image data sequences captured at railway stations and at high ways in large cities. The motion vectors may be used to devise a polar plot (showing velocity magnitude and direction for moving objects where the dominant motion tendency can be seen. The experimental results of comparison of the new motion estimation methods with other well known block matching methods (full search, 2D-log, method based on conventional (cross correlation (CC function or phase correlation (PC function for application of crowd motion estimation are also presented.

Rapid myelin water imaging in human cervical spinal cord.

Science.gov (United States)

Ljungberg, Emil; Vavasour, Irene; Tam, Roger; Yoo, Youngjin; Rauscher, Alexander; Li, David K B; Traboulsee, Anthony; MacKay, Alex; Kolind, Shannon

2017-10-01

Myelin water imaging (MWI) using multi-echo T 2 relaxation is a quantitative MRI technique that can be used as an in vivo biomarker for myelin in the central nervous system. MWI using a multi-echo spin echo sequence currently takes more than 20 min to acquire eight axial slices (5 mm thickness) in the cervical spinal cord, making spinal cord MWI impractical for implementation in clinical studies. In this study, an accelerated gradient and spin echo sequence (GRASE), previously validated for brain MWI, was adapted for spinal cord MWI. Ten healthy volunteers were scanned with the GRASE sequence (acquisition time 8.5 min) and compared with the multi-echo spin echo sequence (acquisition time 23.5 min). Using region of interest analysis, myelin estimates obtained from the two sequences were found to be in good agreement (mean difference = -0.0092, 95% confidence interval =  - 0.0092 ± 0.061; regression slope = 1.01, ρ = 0.9). MWI using GRASE was shown to be highly reproducible with an average coefficient of variation of 6.1%. The results from this study show that MWI can be performed in the cervical spinal cord in less than 10 min, allowing for practical implementation in multimodal clinical studies. Magn Reson Med 78:1482-1487, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

A Stochastic Approach for Blurred Image Restoration and Optical Flow Computation on Field Image Sequence

Institute of Scientific and Technical Information of China (English)

高文; 陈熙霖

1997-01-01

The blur in target images caused by camera vibration due to robot motion or hand shaking and by object(s) moving in the background scene is different to deal with in the computer vision system.In this paper,the authors study the relation model between motion and blur in the case of object motion existing in video image sequence,and work on a practical computation algorithm for both motion analysis and blut image restoration.Combining the general optical flow and stochastic process,the paper presents and approach by which the motion velocity can be calculated from blurred images.On the other hand,the blurred image can also be restored using the obtained motion information.For solving a problem with small motion limitation on the general optical flow computation,a multiresolution optical flow algoritm based on MAP estimation is proposed. For restoring the blurred image ,an iteration algorithm and the obtained motion velocity are used.The experiment shows that the proposed approach for both motion velocity computation and blurred image restoration works well.

Limited-sequence magnetic resonance imaging in the evaluation of the ultrasonographically indeterminate pelvic mass

International Nuclear Information System (INIS)

Chang, S.D.; Cooperberg, P.L.; Wong, A.D.; Llewellyn, P.A.; Bilbey, J.H.

2004-01-01

To evaluate the usefulness of limited-sequence magnetic resonance imaging (MRI) in the elucidation of ultrasonographically indeterminate pelvic masses. This study focused only on pelvic masses in which the origin of the mass (uterine v. extrauterine) could not be determined by ultrasonography (US). The origin of a pelvic mass has clinical implications. A mass arising from the uterus is most likely to be a leiomyoma, which is a benign lesion, whereas an extrauterine mass will have a higher likelihood of malignancy and usually requires surgery. Eighty-one female patients whose pelvic mass was of indeterminate origin on US also underwent limited-sequence MRI of the pelvis. Most of the MRI examinations were performed on the same day as the US. Limited-sequence MRI sequences included a quick gradient-echoT 1 -weighted localizer and a fast spin-echoT 2 -weighted sequence. Final diagnoses were established by surgical pathology or by clinical and imaging follow-up. Limited-sequence MRI was helpful in 79 of the 81 cases (98%). Fifty-two of the 81 masses (64%) were leiomyomas. One was a leiomyosarcoma. The extrauterine masses (26/81 [32%]) were identified as 14 ovarian malignancies, 4 endometriomas, 3 dermoids, an ovarian fibroma, an infarcted fibrothecoma, an infarcted hemorrhagic cyst, a sigmoid diverticular abscess and a gastrointestinal stromal tumour of the ileum. In the other 2 cases (2/81 [2%]), the origin of the pelvic mass remained indeterminate. Both of these indeterminate masses showed low signal onT 2 -weighted images and were interpreted as probable leiomyomas. They were not surgically removed but were followed clinically and had a stable course. Limited-sequence MRI is a quick and efficient way to further evaluate ultrasonographically indeterminate pelvic masses. Limited-sequence MRI of the pelvis can suffice, in these cases, without requiring a full MRI examination. (author)

Limited-sequence magnetic resonance imaging in the evaluation of the ultrasonographically indeterminate pelvic mass

Energy Technology Data Exchange (ETDEWEB)

Chang, S.D. [Univ. of British Columbia, Vancouver Hospital and Helath Services Centre, Dept. of Radiology, Vancouver, British Columbia (Canada)]. E-mail: schang@vanhosp.bc.ca; Cooperberg, P.L.; Wong, A.D. [Univ. of British Columbia, St. Paul' s Hospital, Dept. of Radiology, Vancouver, British Columbia (Canada); Llewellyn, P.A. [Lion' s Gate Hospital, Dept. of Radiology, North Vancouver, British Columbia (Canada); Bilbey, J.H. [Royal Inland Hospital, Dept. of Radiology, Kamloops, British Columbia (Canada)

2004-04-01

To evaluate the usefulness of limited-sequence magnetic resonance imaging (MRI) in the elucidation of ultrasonographically indeterminate pelvic masses. This study focused only on pelvic masses in which the origin of the mass (uterine v. extrauterine) could not be determined by ultrasonography (US). The origin of a pelvic mass has clinical implications. A mass arising from the uterus is most likely to be a leiomyoma, which is a benign lesion, whereas an extrauterine mass will have a higher likelihood of malignancy and usually requires surgery. Eighty-one female patients whose pelvic mass was of indeterminate origin on US also underwent limited-sequence MRI of the pelvis. Most of the MRI examinations were performed on the same day as the US. Limited-sequence MRI sequences included a quick gradient-echoT{sub 1}-weighted localizer and a fast spin-echoT{sub 2}-weighted sequence. Final diagnoses were established by surgical pathology or by clinical and imaging follow-up. Limited-sequence MRI was helpful in 79 of the 81 cases (98%). Fifty-two of the 81 masses (64%) were leiomyomas. One was a leiomyosarcoma. The extrauterine masses (26/81 [32%]) were identified as 14 ovarian malignancies, 4 endometriomas, 3 dermoids, an ovarian fibroma, an infarcted fibrothecoma, an infarcted hemorrhagic cyst, a sigmoid diverticular abscess and a gastrointestinal stromal tumour of the ileum. In the other 2 cases (2/81 [2%]), the origin of the pelvic mass remained indeterminate. Both of these indeterminate masses showed low signal onT{sub 2}-weighted images and were interpreted as probable leiomyomas. They were not surgically removed but were followed clinically and had a stable course. Limited-sequence MRI is a quick and efficient way to further evaluate ultrasonographically indeterminate pelvic masses. Limited-sequence MRI of the pelvis can suffice, in these cases, without requiring a full MRI examination. (author)

Magnetic resonance imaging (MRI) of articular cartilage of the knee using ultrashort echo time (uTE) sequences with spiral acquisition

International Nuclear Information System (INIS)

Goto, Hajimu; Fujii, Masahiko; Iwama, Yuki; Aoyama, Nobukazu; Ohno, Yoshiharu; Sugimura, Kazuro

2012-01-01

The objective of this study was to evaluate the sensitivity of ultrashort echo time (uTE) sequence for visualisation of calcified deep layers of articular cartilage. MRI with a uTE sequence was performed on five healthy volunteers. Signals from the calcified deep layers of the articular knee cartilage were evaluated on uTE subtraction images and computed tomography images. The calcified deep layers of the articular cartilage changed from having a low to a high signal when imaged with a uTE sequence. The reported uTE sequence was effective in imaging the deep layers of the knee cartilage.

Rapid hyperspectral image classification to enable autonomous search systems

Directory of Open Access Journals (Sweden)

Raj Bridgelal

2016-11-01

Full Text Available The emergence of lightweight full-frame hyperspectral cameras is destined to enable autonomous search vehicles in the air, on the ground and in water. Self-contained and long-endurance systems will yield important new applications, for example, in emergency response and the timely identification of environmental hazards. One missing capability is rapid classification of hyperspectral scenes so that search vehicles can immediately take actions to verify potential targets. Onsite verifications minimise false positives and preclude the expense of repeat missions. Verifications will require enhanced image quality, which is achievable by either moving closer to the potential target or by adjusting the optical system. Such a solution, however, is currently impractical for small mobile platforms with finite energy sources. Rapid classifications with current methods demand large computing capacity that will quickly deplete the on-board battery or fuel. To develop the missing capability, the authors propose a low-complexity hyperspectral image classifier that approaches the performance of prevalent classifiers. This research determines that the new method will require at least 19-fold less computing capacity than the prevalent classifier. To assess relative performances, the authors developed a benchmark that compares a statistic of library endmember separability in their respective feature spaces.

Validation of Ion TorrentTM Inherited Disease Panel with the PGMTM Sequencing Platform for Rapid and Comprehensive Mutation Detection

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Abeer E. Mustafa

2018-05-01

Full Text Available Quick and accurate molecular testing is necessary for the better management of many inherited diseases. Recent technological advances in various next generation sequencing (NGS platforms, such as target panel-based sequencing, has enabled comprehensive, quick, and precise interrogation of many genetic variations. As a result, these technologies have become a valuable tool for gene discovery and for clinical diagnostics. The AmpliSeq Inherited Disease Panel (IDP consists of 328 genes underlying more than 700 inherited diseases. Here, we aimed to assess the performance of the IDP as a sensitive and rapid comprehensive gene panel testing. A total of 88 patients with inherited diseases and causal mutations that were previously identified by Sanger sequencing were randomly selected for assessing the performance of the IDP. The IDP successfully detected 93.1% of the mutations in our validation cohort, achieving high overall gene coverage (98%. The sensitivity for detecting single nucleotide variants (SNVs and short Indels was 97.3% and 69.2%, respectively. IDP, when coupled with Ion Torrent Personal Genome Machine (PGM, delivers comprehensive and rapid sequencing for genes that are responsible for various inherited diseases. Our validation results suggest the suitability of this panel for use as a first-line screening test after applying the necessary clinical validation.

Parry-Romberg syndrome: findings in advanced magnetic resonance imaging sequences - case report

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Paula, Rafael Alfenas de; Ribeiro, Bruno Niemeyer de Freitas, E-mail: alfenas85@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Hospital Universitario Clementino Fraga Filho; Bahia, Paulo Roberto Valle [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Dept. de radiologia; Ribeiro, Renato Niemeyer de Freitas [Hospital de Clinica de Jacarepagua, Rio de Janeiro, RJ (Brazil); Carvalho, Lais Balbi de [Universidade Presidente Antonio Carlos (Unipac), Juiz de Fora, MG (Brazil)

2014-05-15

Parry-Romberg syndrome is a rare disease characterized by progressive hemifacial atrophy associated with other systemic changes, including neurological symptoms. Currently, there are few studies exploring the utilization of advanced magnetic resonance sequences in the investigation of this disease. The authors report the case of a 45-year-old patient and describe the findings at structural magnetic resonance imaging and at advanced sequences, correlating them with pathophysiological data. (author)

Protocol optimization of sacroiliac joint MR Imaging at 3 Tesla: Impact of coil design and motion resistant sequences on image quality.

Science.gov (United States)

Gondim Teixeira, P A; Bravetti, M; Hossu, G; Lecocq, S; Petit, D; Loeuille, D; Blum, A

2017-12-01

To evaluate the impact of coil design and motion-resistant sequences on the quality of sacroiliac magnetic resonance imaging (MRI) examination in patients with spondyloarthropathy. One hundred and twenty-one patients with suspected sacroiliitis and referred for MRI of the sacroiliac joints were retrospectively evaluated with MRI at 3-Tesla. There were 78 women and 43 men with a mean age of 36.7±11.5 (SD) years (range: 15.8-78.4 years). Conventional and motion-resistant fat-saturated fast-spin echo T2-weighted sequences were performed with two different coils. Image quality was subjectively evaluated by two independent readers (R1 and R2) using a four-point scale. Confidence in the identification of bone marrow edema pattern (BMEP) was also evaluated subjectively using a three-point scale. Phased array body coil yielded improved image quality compared to surface coil (14.1 to 30.4% for R1 and 14.6 to 25.7% for R2; Pcoil with motion-resistant T2-weighted sequence (kappa 0.990). The smallest number of indeterminate BMEP zones was seen on MRI set acquired with the phased-array body coil and motion-resistant T2-weighted sequence. Phased array body coil and motion-resistant T2-weighted sequences perform better than surface coil and conventional T2-weighted sequences for the evaluation of sacroiliac joints, increasing confidence in the identification of BMEP. Copyright © 2017 Editions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

Three-dimensional gradient echo versus spin echo sequence in contrast-enhanced imaging of the pituitary gland at 3 T

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Kakite, Suguru, E-mail: sugkaki@med.tottori-u.ac.jp [Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8503 (Japan); Fujii, Shinya [Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8503 (Japan); Kurosaki, Masamichi [Department of Neurosurgery, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8503 (Japan); Kanasaki, Yoshiko; Matsusue, Eiji; Kaminou, Toshio; Ogawa, Toshihide [Division of Radiology, Department of Pathophysiological and Therapeutic Science, Faculty of Medicine, Tottori University, 36-1, Nishicho, Yonago 683-8503 (Japan)

2011-07-15

Introduction: To clarify whether a three-dimensional-gradient echo (3D-GRE) or spin echo (SE) sequence is more useful for evaluating sellar lesions on contrast-enhanced T1-weighted MR imaging at 3.0 Tesla (T). Methods: We retrospectively assessed contrast-enhanced T1-weighted images using 3D-GRE and SE sequences at 3.0 T obtained from 33 consecutive patients with clinically suspected sellar lesions. Two experienced neuroradiologists evaluated the images qualitatively in terms of the following criteria: boundary edge of the cavernous sinus and pituitary gland, border of sellar lesions, delineation of the optic nerve and cranial nerves within the cavernous sinus, susceptibility and flow artifacts, and overall image quality. Results: At 3.0 T, 3D-GRE provided significantly better images than the SE sequence in terms of the border of sellar lesions, delineation of cranial nerves, and overall image quality; there was no significant difference regarding the boundary edge of the cavernous sinus and pituitary gland. In addition, the 3D-GRE sequence showed fewer pulsation artifacts but more susceptibility artifacts. Conclusion: Our results indicate that 3D-GRE is the more suitable sequence for evaluating sellar lesions on contrast-enhanced T1-weighted imaging at 3.0 T.

Rapid focused sequencing: a multiplexed assay for simultaneous detection and strain typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis.

Directory of Open Access Journals (Sweden)

Rosemary S Turingan

Full Text Available BACKGROUND: The intentional release of Bacillus anthracis in the United States in 2001 has heightened concern about the use of pathogenic microorganisms in bioterrorism attacks. Many of the deadliest bacteria, including the Class A Select Agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis, are highly infectious via the pulmonary route when released in aerosolized form. Hence, rapid, sensitive, and reliable methods for detection of these biothreats and characterization of their potential impact on the exposed population are of critical importance to initiate and support rapid military, public health, and clinical responses. METHODOLOGY/PRINCIPAL FINDINGS: We have developed microfluidic multiplexed PCR and sequencing assays based on the simultaneous interrogation of three pathogens per assay and ten loci per pathogen. Microfluidic separation of amplified fluorescently labeled fragments generated characteristic electrophoretic signatures for identification of each agent. The three sets of primers allowed significant strain typing and discrimination from non-pathogenic closely-related species and environmental background strains based on amplicon sizes alone. Furthermore, sequencing of the 10 amplicons per pathogen, termed "Rapid Focused Sequencing," allowed an even greater degree of strain discrimination and, in some cases, can be used to determine virulence. Both amplification and sequencing assays were performed in microfluidic biochips developed for fast thermal cycling and requiring 7 µL per reaction. The 30-plex sequencing assay resulted in genotypic resolution of 84 representative strains belonging to each of the three biothreat species. CONCLUSIONS/SIGNIFICANCE: The microfluidic multiplexed assays allowed identification and strain differentiation of the biothreat agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis and clear discrimination from closely-related species and several environmental

[Contrastive analysis of artifacts produced by metal dental crowns in 3.0 T magnetic resonance imaging with six sequences].

Science.gov (United States)

Lan, Gao; Yunmin, Lian; Pu, Wang; Haili, Huai

2016-06-01

This study aimed to observe and evaluate six 3.0 T sequences of metallic artifacts produced by metal dental crowns. Dental crowns fabricated with four different materials (Co-Gr, Ni-Gr, Ti alloy and pure Ti) were evaluated. A mature crossbreed dog was used as the experimental animal, and crowns were fabricated for its upper right second premolar. Each crown was examined through head MRI (3.0 T) with six sequences, namely, T₁ weighted-imaging of spin echo (T₁W/SE), T₂ weighted-imaging of inversion recovery (T₂W/IR), T₂ star gradient echo (T₂*/GRE), T2 weighted-imaging of fast spin echo (T₂W/FSE), T₁ weighted-imaging of fluid attenuate inversion recovery (T₂W/FLAIR), and T₂ weighted-imaging of propeller (T₂W/PROP). The largest area and layers of artifacts were assessed and compared. The artifact in the T₂*/GRE sequence was significantly wider than those in the other sequences (P 0.05). T₂*/GRE exhibit the strongest influence on the artifact, whereas the five other sequences contribute equally to artifact generation.

Simulation and Efficient Measurements of Intensities for Complex Imaging Sequences

DEFF Research Database (Denmark)

Jensen, Jørgen Arendt; Rasmussen, Morten Fischer; Stuart, Matthias Bo

2014-01-01

on the sequence to simulate both intensity and mechanical index (MI) according to FDA rules. A 3 MHz BK Medical 8820e convex array transducer is used with the SARUS scanner. An Onda HFL-0400 hydrophone and the Onda AIMS III system measures the pressure field for three imaging schemes: a fixed focus, single...

Managing complex processing of medical image sequences by program supervision techniques

Science.gov (United States)

Crubezy, Monica; Aubry, Florent; Moisan, Sabine; Chameroy, Virginie; Thonnat, Monique; Di Paola, Robert

1997-05-01

Our objective is to offer clinicians wider access to evolving medical image processing (MIP) techniques, crucial to improve assessment and quantification of physiological processes, but difficult to handle for non-specialists in MIP. Based on artificial intelligence techniques, our approach consists in the development of a knowledge-based program supervision system, automating the management of MIP libraries. It comprises a library of programs, a knowledge base capturing the expertise about programs and data and a supervision engine. It selects, organizes and executes the appropriate MIP programs given a goal to achieve and a data set, with dynamic feedback based on the results obtained. It also advises users in the development of new procedures chaining MIP programs.. We have experimented the approach for an application of factor analysis of medical image sequences as a means of predicting the response of osteosarcoma to chemotherapy, with both MRI and NM dynamic image sequences. As a result our program supervision system frees clinical end-users from performing tasks outside their competence, permitting them to concentrate on clinical issues. Therefore our approach enables a better exploitation of possibilities offered by MIP and higher quality results, both in terms of robustness and reliability.

Nosocomial rapidly growing mycobacterial infections following laparoscopic surgery: CT imaging findings.

Science.gov (United States)

Volpato, Richard; de Castro, Claudio Campi; Hadad, David Jamil; da Silva Souza Ribeiro, Flavya; Filho, Ezequiel Leal; Marcal, Leonardo P

2015-09-01

To identify the distribution and frequency of computed tomography (CT) findings in patients with nosocomial rapidly growing mycobacterial (RGM) infection after laparoscopic surgery. A descriptive retrospective study in patients with RGM infection after laparoscopic surgery who underwent CT imaging prior to initiation of therapy. The images were analyzed by two radiologists in consensus, who evaluated the skin/subcutaneous tissues, the abdominal wall, and intraperitoneal region separately. The patterns of involvement were tabulated as: densification, collections, nodules (≥1.0 cm), small nodules (<1.0 cm), pseudocavitated nodules, and small pseudocavitated nodules. Twenty-six patients met the established criteria. The subcutaneous findings were: densification (88.5%), small nodules (61.5%), small pseudocavitated nodules (23.1 %), nodules (38.5%), pseudocavitated nodules (15.4%), and collections (26.9%). The findings in the abdominal wall were: densification (61.5%), pseudocavitated nodules (3.8%), and collections (15.4%). The intraperitoneal findings were: densification (46.1%), small nodules (42.3%), nodules (15.4%), and collections (11.5%). Subcutaneous CT findings in descending order of frequency were: densification, small nodules, nodules, small pseudocavitated nodules, pseudocavitated nodules, and collections. The musculo-fascial plane CT findings were: densification, collections, and pseudocavitated nodules. The intraperitoneal CT findings were: densification, small nodules, nodules, and collections. • Rapidly growing mycobacterial infection may occur following laparoscopy. • Post-laparoscopy mycobacterial infection CT findings are densification, collection, and nodules. • Rapidly growing mycobacterial infection following laparoscopy may involve the peritoneal cavity. • Post-laparoscopy rapidly growing mycobacterial intraperitoneal infection is not associated with ascites or lymphadenopathy.

Rapid musculoskeletal magnetic resonance imaging using integrated parallel acquisition techniques (IPAT) - Initial experiences

International Nuclear Information System (INIS)

Romaneehsen, B.; Oberholzer, K.; Kreitner, K.-F.; Mueller, L.P.

2003-01-01

Purpose: To investigate the feasibility of using multiple receiver coil elements for time saving integrated parallel imaging techniques (iPAT) in traumatic musculoskeletal disorders. Material and methods: 6 patients with traumatic derangements of the knee, ankle and hip underwent MR imaging at 1.5 T. For signal detection of the knee and ankle, we used a 6-channel body array coil that was placed around the joints, for hip imaging two 4-channel body array coils and two elements of the spine array coil were combined for signal detection. All patients were investigated with a standard imaging protocol that mainly consisted of different turbo spin-echo sequences (PD-, T 2 -weighted TSE with and without fat suppression, STIR). All sequences were repeated with an integrated parallel acquisition technique (iPAT) using a modified sensitivity encoding (mSENSE) technique with an acceleration factor of 2. Overall image quality was subjectively assessed using a five-point scale as well as the ability for detection of pathologic findings. Results: Regarding overall image quality, there were no significant differences between standard imaging and imaging using mSENSE. All pathologies (occult fracture, meniscal tear, torn and interpositioned Hoffa's cleft, cartilage damage) were detected by both techniques. iPAT led to a 48% reduction of acquisition time compared with standard technique. Additionally, time savings with iPAT led to a decrease of pain-induced motion artifacts in two cases. Conclusion: In times of increasing cost pressure, iPAT using multiple coil elements seems to be an efficient and economic tool for fast musculoskeletal imaging with diagnostic performance comparable to conventional techniques. (orig.) [de

Centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo sequence: improvement of the image quality of oxygen-enhanced MRI

International Nuclear Information System (INIS)

Ohno, Yoshiharu; Hatabu, Hiroto; Higashino, Takanori; Kawamitsu, Hideaki; Watanabe, Hirokazu; Takenaka, Daisuke; Cauteren, Marc van; Sugimura, Kazuro

2004-01-01

Purpose: The purpose of the study presented here was to determine the improvement in image quality of oxygen-enhanced magnetic resonance (MR) subtraction imaging obtained with a centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo (c-IR-HASTE) sequence compared with that obtained with a conventional sequentially reordered inversion recovery single-shot HASTE (s-IR-HASTE) sequence for pulmonary imaging. Materials and methods: Oxygen-enhanced MR imaging using a 1.5 T whole body scanner was performed on 12 healthy, non-smoking volunteers. Oxygen-enhanced MR images were obtained with the coronal two-dimensional (2D) c-IR-HASTE sequence and 2D s-IR-HASTE sequence combined with respiratory triggering. For a 256x256 matrix, 132 phase-encoding steps were acquired including four steps for phase correction. Inter-echo spacing for each sequence was 4.0 ms. The effective echo time (TE) for c-IR-HASTE was 4.0 ms, and 16 ms for s-IR-HASTE. The inversion time (TI) was 900 ms. To determine the improvement in oxygen-enhanced MR subtraction imaging by c-IR-HASTE, CNRs of subtraction image, overall image quality, and image degradation of the c-IR-HASTE and s-IR-HASTE techniques were statistically compared. Results: CNR, overall image quality, and image degradation of c-IR-HASTE images showed significant improvement compared to those s-IR-HASTE images (P<0.05). Conclusion: Centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo (c-IR-HASTE) sequence enhanced the signal from the lung and improved the image quality of oxygen-enhanced MR subtraction imaging

RECOGNITION OF DRAINAGE TUNNELS DURING GLACIER LAKE OUTBURST EVENTS FROM TERRESTRIAL IMAGE SEQUENCES

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E. Schwalbe

2016-06-01

Full Text Available In recent years, many glaciers all over the world have been distinctly retreating and thinning. One of the consequences of this is the increase of so called glacier lake outburst flood events (GLOFs. The mechanisms ruling such GLOF events are still not yet fully understood by glaciologists. Thus, there is a demand for data and measurements that can help to understand and model the phenomena. Thereby, a main issue is to obtain information about the location and formation of subglacial channels through which some lakes, dammed by a glacier, start to drain. The paper will show how photogrammetric image sequence analysis can be used to collect such data. For the purpose of detecting a subglacial tunnel, a camera has been installed in a pilot study to observe the area of the Colonia Glacier (Northern Patagonian Ice Field where it dams the Lake Cachet II. To verify the hypothesis, that the course of the subglacial tunnel is indicated by irregular surface motion patterns during its collapse, the camera acquired image sequences of the glacier surface during several GLOF events. Applying tracking techniques to these image sequences, surface feature motion trajectories could be obtained for a dense raster of glacier points. Since only a single camera has been used for image sequence acquisition, depth information is required to scale the trajectories. Thus, for scaling and georeferencing of the measurements a GPS-supported photogrammetric network has been measured. The obtained motion fields of the Colonia Glacier deliver information about the glacier’s behaviour before during and after a GLOF event. If the daily vertical glacier motion of the glacier is integrated over a period of several days and projected into a satellite image, the location and shape of the drainage channel underneath the glacier becomes visible. The high temporal resolution of the motion fields may also allows for an analysis of the tunnels dynamic in comparison to the changing

Imaging of cranial nerves with three-dimensional high resolution diffusion-weighted MR sequence based on SSFP technique

International Nuclear Information System (INIS)

Zhang Zhongwei; Chen Yingming; Meng Quanfei

2008-01-01

Objective: To depict the normal anatomy of cranial nerves in detail and define the exact relationships between cranial nerves and adjacent structures with three-dimensional high resolution diffusion-weighted MR sequence based on SSFP technique (3D DW-SSFP). Methods: 3D DW- SSFP sequence was performed and axial images were obtained in 12 healthy volunteers Post-processing techniques were used to generate images of cranial nerves, and the images acquired were compared with anatomical sections and diagrams of textbook. Results: In all subjects, 3D DW-SSFP sequence could produce homogeneous images and high contrast between the cranial nerves and other solid structures. The intracranial portions of all cranial nerves except olfactory nerve were identified; the extracranial portions of nerve Ⅱ-Ⅻ were identified in all subjects bilaterally. Conclusion: The 3D DW-SSFP sequence can characterize the normal MR appearance of cranial nerves and its branches and the ability to define the nerves may provide greater sensitivity and specificity in detecting abnormalities of craniofacial structure. (authors)

Pulse sequence optimization for superparamagnetic iron oxide-enhaced MR imaging in the detection of hepatic VX2 tumors in rabbits

International Nuclear Information System (INIS)

Jang, Hyun Jung; Han, Joon Koo; Lee, Kyoung Ho; Kim, Se Hyung; Choi, Byung Ihn; Kim, Tae Kyoung

2003-01-01

The purpose of this experimental study was to determine the optimal pulse sequences for SPIO-enhanced MR imaging in the evaluation of multiple hepatic tumors. Twelve rabbits with multiple VX2 liver tumors underwent SPOI-enhanced MRI using the following nine pulse sequences: TSE T2-weighted imaging (T2W1), TSE proton density-weighted imaging(PDWI), and GRE T2*-weighted imaging (T2*W1) with seven different echo times (TE). Liver-lesion contrast-to-noise ratios (CNRs) were calculated, and images were also assessed qualitatively by two radiologists, who reached a consensus as to lesion conspicuity and imaging artifacts using a four-level scale. By means of pathologic correlation, the sensitivity and positive predictive value of each sequence was calculated. TSE T2W1 and long-TE (35 msec) FLASH T2*W1 showed the highest liver-lesion CNR. The best lesion conspicuity was seen at TSE T2W1 and medium-TE (12 msec) GRE T2*W1. Short TE GRE T2*W1 showed the least imaging artifacts. The four sequences which demonstrated the best sensitivity were medium-TE (12 msec), GRE T2*W1 (FLASH, 84%; FISP, 82%), TSE W2T1 (79%), and TSE PDWI (76%). All nine sequences showed overall high positive predictive value (86-97%), with no statistically significant difference (p>0.05). In terms of image quality and the detection of sensitivity, TSE T2W1 and medium TE (12 msec) GRE T2*W1 were the top two pulse sequences among the various sequences used for no SPIO-enhanced MRI. They are thus considered to be optimal sequences for evaluating multiple malignant hepatic tumors

Magnetic resonance imaging of single rice kernels during cooking

NARCIS (Netherlands)

Mohoric, A.; Vergeldt, F.J.; Gerkema, E.; Jager, de P.A.; Duynhoven, van J.P.M.; Dalen, van G.; As, van H.

2004-01-01

The RARE imaging method was used to monitor the cooking of single rice kernels in real time and with high spatial resolution in three dimensions. The imaging sequence is optimized for rapid acquisition of signals with short relaxation times using centered out RARE. Short scan time and high spatial

A novel color image encryption scheme using fractional-order hyperchaotic system and DNA sequence operations

International Nuclear Information System (INIS)

Zhang Li-Min; Sun Ke-Hui; Liu Wen-Hao; He Shao-Bo

2017-01-01

In this paper, Adomian decomposition method (ADM) with high accuracy and fast convergence is introduced to solve the fractional-order piecewise-linear (PWL) hyperchaotic system. Based on the obtained hyperchaotic sequences, a novel color image encryption algorithm is proposed by employing a hybrid model of bidirectional circular permutation and DNA masking. In this scheme, the pixel positions of image are scrambled by circular permutation, and the pixel values are substituted by DNA sequence operations. In the DNA sequence operations, addition and substraction operations are performed according to traditional addition and subtraction in the binary, and two rounds of addition rules are used to encrypt the pixel values. The simulation results and security analysis show that the hyperchaotic map is suitable for image encryption, and the proposed encryption algorithm has good encryption effect and strong key sensitivity. It can resist brute-force attack, statistical attack, differential attack, known-plaintext, and chosen-plaintext attacks. (paper)

Eigenimage filtering of nuclear medicine image sequences

International Nuclear Information System (INIS)

Windham, J.P.; Froelich, J.W.; Abd-Allah, M.

1985-01-01

In many nuclear medicine imaging sequences the localization of radioactivity in organs other than the target organ interferes with imaging of the desired anatomical structure or physiological process. A filtering technique has been developed which suppresses the interfering process while enhancing the desired process. This technique requires the identification of temporal sequential signatures for both the interfering and desired processes. These signatures are placed in the form of signature vectors. Signature matrices, M/sub D/ and M/sub U/, are formed by taking the outer product expansion of the temporal signature vectors for the desired and interfering processes respectively. By using the transformation from the simultaneous diagonalization of these two signature matrices a weighting vector is obtained. The technique is shown to maximize the projection of the desired process while minimizing the interfering process based upon an extension of Rayleigh's Principle. The technique is demonstrated for first pass renal and cardiac flow studies. This filter offers a potential for simplifying and extending the accuracy of diagnostic nuclear medicine procedures

Hyperspectral image analysis for rapid and accurate discrimination of bacterial infections: A benchmark study.

Science.gov (United States)

Arrigoni, Simone; Turra, Giovanni; Signoroni, Alberto

2017-09-01

With the rapid diffusion of Full Laboratory Automation systems, Clinical Microbiology is currently experiencing a new digital revolution. The ability to capture and process large amounts of visual data from microbiological specimen processing enables the definition of completely new objectives. These include the direct identification of pathogens growing on culturing plates, with expected improvements in rapid definition of the right treatment for patients affected by bacterial infections. In this framework, the synergies between light spectroscopy and image analysis, offered by hyperspectral imaging, are of prominent interest. This leads us to assess the feasibility of a reliable and rapid discrimination of pathogens through the classification of their spectral signatures extracted from hyperspectral image acquisitions of bacteria colonies growing on blood agar plates. We designed and implemented the whole data acquisition and processing pipeline and performed a comprehensive comparison among 40 combinations of different data preprocessing and classification techniques. High discrimination performance has been achieved also thanks to improved colony segmentation and spectral signature extraction. Experimental results reveal the high accuracy and suitability of the proposed approach, driving the selection of most suitable and scalable classification pipelines and stimulating clinical validations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Detection of hepatic VX2 carcinomas with ferucarbotran-enhanced magnetic resonance imaging in rabbits: Comparison of nine pulse sequences

International Nuclear Information System (INIS)

Kim, Seong Hyun; Choi, Dongil; Lim, Hyo K.; Kim, Min Ju; Jang, Kyung Mi; Kim, Seung Hoon; Lee, Won Jae; Lee, Jongmee; Jeon, Yong Hwan; Lim, Jae Hoon

2006-01-01

Objective: To compare the diagnostic performance of a variety of magnetic resonance imaging (MRI) sequences, in order to identify the most effective ferucarbotran-enhanced sequence for the detection of multiple small hepatic VX2 carcinomas in rabbits. Methods: Fifteen rabbits with experimentally induced 135 VX2 carcinomas in the liver underwent ferucarbotran-enhanced MRI using the following nine pulse sequences: a fat-suppressed fast spin-echo (FSE) sequence with two echo times (TE) (proton density- and T2-weighted images), four different T2*-weighted fast multiplanar GRASS (gradient-recalled acquisition in the steady state) (FMPGR) with the combination of three TEs (9, 12, 15 ms, respectively) and two flip angles (20 deg., 80 deg., respectively), T2*-weighted fast multiplanar spoiled GRASS (FMPSPGR), T1-weighted FMPSPGR, and dynamic T1-weighted FMPSPGR. All images were reviewed by three radiologists with quantitative and qualitative analysis. Results: Tumor-to-liver contrast-to-noise ratio of the proton density-weighted FSE sequence was significantly higher than those of the others (p o ) images were superior to those of the others and for the detection of very small hepatic tumors of less than 5 mm, the sensitivities of these sequences were less than 30%. Conclusion: Ferucarbotran-enhanced T2- and proton density-weighted FSE and T2*-weighed FMPGR (TE/flip angle, 12/20 o ) images were found to be the most effective pulse sequences for the detection of multiple small hepatic VX2 carcinomas but these sequences were limited in the detection of very small hepatic tumors of less than 5 mm in size

Pressure applied by the healthcare staff on a cricoids cartilage simulator during Sellick's maneuver in rapid sequence intubation

NARCIS (Netherlands)

J.A. Calvache (Jose Andrés); L.C.B. Sandoval (Luz); W.A. Vargas (William Andres)

2013-01-01

textabstractBackground: Sellick's maneuver or cricoid pressure is a strategy used to prevent bronchoaspiration during the rapid intubation sequence. Several studies have described that the force required for an adequate maneuver is of 2.5-3.5 kg. The purpose of this paper was to determine the force

MR imaging at 0.5 Tesla with FLAIR sequence in the diagnosis of acute subarachnoid hemorrhage

International Nuclear Information System (INIS)

Kopsa, W.; Leitner, H.; Tscholakoff, D.; Perneczky, G.

1998-01-01

Purpose: Evaluation of MR imaging in patients with acute subarachnoid hemorrhage (SAH) at 0.5 Tesla using the FLAIR (Fluid Attenuated Inversion Recovery) sequenze. Additionally, the value of MR angiographie (MRA) in the diagnosis of intracranial aneurysms was assessed. Materials and Methods: 19 patients with suspected acute SAH were included in this study. MR imaging was performed using an axial FLAIR sequence and axial T 1 , T 2 and PD weighted sequences. In 16 patients an additional MRA (3D-TOF) was performed. 10 patients without SAH were examined as a control group. At the end of the study the 29 MR examinations were randomised and the images were read by two experienced radiologists; subsequently a consensus interpretation was made. Results: In 16 patients an acute SAH was verified with the FLAIR sequence, in 13 cases the origin of hemorrhage was found during surgery. In the consensus interpretation of the MR images all cases were diagnosed properly. 12 of the 16 MRA studies were of diagnostic quality, but only 6 cases were interpreted correctly. Conclusion: The FLAIR sequence at 0.5 Tesla proved effective in the diagnosis of acute SAH. MRA at 0.5 Tesla failed in the detection of intracranial aneurysms. (orig.) [de

Optimization of an on-board imaging system for extremely rapid radiation therapy

International Nuclear Information System (INIS)

Cherry Kemmerling, Erica M.; Wu, Meng; Yang, He; Fahrig, Rebecca; Maxim, Peter G.; Loo, Billy W.

2015-01-01

Purpose: Next-generation extremely rapid radiation therapy systems could mitigate the need for motion management, improve patient comfort during the treatment, and increase patient throughput for cost effectiveness. Such systems require an on-board imaging system that is competitively priced, fast, and of sufficiently high quality to allow good registration between the image taken on the day of treatment and the image taken the day of treatment planning. In this study, three different detectors for a custom on-board CT system were investigated to select the best design for integration with an extremely rapid radiation therapy system. Methods: Three different CT detectors are proposed: low-resolution (all 4 × 4 mm pixels), medium-resolution (a combination of 4 × 4 mm pixels and 2 × 2 mm pixels), and high-resolution (all 1 × 1 mm pixels). An in-house program was used to generate projection images of a numerical anthropomorphic phantom and to reconstruct the projections into CT datasets, henceforth called “realistic” images. Scatter was calculated using a separate Monte Carlo simulation, and the model included an antiscatter grid and bowtie filter. Diagnostic-quality images of the phantom were generated to represent the patient scan at the time of treatment planning. Commercial deformable registration software was used to register the diagnostic-quality scan to images produced by the various on-board detector configurations. The deformation fields were compared against a “gold standard” deformation field generated by registering initial and deformed images of the numerical phantoms that were used to make the diagnostic and treatment-day images. Registrations of on-board imaging system data were judged by the amount their deformation fields differed from the corresponding gold standard deformation fields—the smaller the difference, the better the system. To evaluate the registrations, the pointwise distance between gold standard and realistic registration

Optimization of an on-board imaging system for extremely rapid radiation therapy

Energy Technology Data Exchange (ETDEWEB)

Cherry Kemmerling, Erica M.; Wu, Meng, E-mail: mengwu@stanford.edu; Yang, He; Fahrig, Rebecca [Department of Radiology, Stanford University, Stanford, California 94305 (United States); Maxim, Peter G.; Loo, Billy W. [Department of Radiation Oncology, Stanford University, Stanford, California 94305 and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305 (United States)

2015-11-15

Purpose: Next-generation extremely rapid radiation therapy systems could mitigate the need for motion management, improve patient comfort during the treatment, and increase patient throughput for cost effectiveness. Such systems require an on-board imaging system that is competitively priced, fast, and of sufficiently high quality to allow good registration between the image taken on the day of treatment and the image taken the day of treatment planning. In this study, three different detectors for a custom on-board CT system were investigated to select the best design for integration with an extremely rapid radiation therapy system. Methods: Three different CT detectors are proposed: low-resolution (all 4 × 4 mm pixels), medium-resolution (a combination of 4 × 4 mm pixels and 2 × 2 mm pixels), and high-resolution (all 1 × 1 mm pixels). An in-house program was used to generate projection images of a numerical anthropomorphic phantom and to reconstruct the projections into CT datasets, henceforth called “realistic” images. Scatter was calculated using a separate Monte Carlo simulation, and the model included an antiscatter grid and bowtie filter. Diagnostic-quality images of the phantom were generated to represent the patient scan at the time of treatment planning. Commercial deformable registration software was used to register the diagnostic-quality scan to images produced by the various on-board detector configurations. The deformation fields were compared against a “gold standard” deformation field generated by registering initial and deformed images of the numerical phantoms that were used to make the diagnostic and treatment-day images. Registrations of on-board imaging system data were judged by the amount their deformation fields differed from the corresponding gold standard deformation fields—the smaller the difference, the better the system. To evaluate the registrations, the pointwise distance between gold standard and realistic registration

Characterization of platelet adhesion under flow using microscopic image sequence analysis.

Science.gov (United States)

Machin, M; Santomaso, A; Cozzi, M R; Battiston, M; Mazzuccato, M; De Marco, L; Canu, P

2005-07-01

A method for quantitative analysis of platelet deposition under flow is discussed here. The model system is based upon perfusion of blood platelets over an adhesive substrate immobilized on a glass coverslip acting as the lower surface of a rectangular flow chamber. The perfusion apparatus is mounted onto an inverted microscope equipped with epifluorescent illumination and intensified CCD video camera. Characterization is based on information obtained from a specific image analysis method applied to continuous sequences of microscopical images. Platelet recognition across the sequence of images is based on a time-dependent, bidimensional, gaussian-like pdf. Once a platelet is located,the variation of its position and shape as a function of time (i.e., the platelet history) can be determined. Analyzing the history we can establish if the platelet is moving on the surface, the frequency of this movement and the distance traveled before its resumes the velocity of a non-interacting cell. Therefore, we can determine how long the adhesion would last which is correlated to the resistance of the platelet-substrate bond. This algorithm enables the dynamic quantification of trajectories, as well as residence times, arrest and release frequencies for a high numbers of platelets at the same time. Statistically significant conclusions on platelet-surface interactions can then be obtained. An image analysis tool of this kind can dramatically help the investigation and characterization of the thrombogenic properties of artificial surfaces such as those used in artificial organs and biomedical devices.

Integration of image guidance and rapid prototyping technology in craniofacial surgery.

Science.gov (United States)

Bullock, P; Dunaway, D; McGurk, L; Richards, R

2013-08-01

This technical note demonstrates the benefits of preoperative planning, involving the use of rapid prototype models and rehearsal of the surgical procedure, using image-guided navigational surgery. Optimum reconstruction of large defects can be achieved with this technique. Copyright © 2013 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Technical Note: Deep learning based MRAC using rapid ultra-short echo time imaging.

Science.gov (United States)

Jang, Hyungseok; Liu, Fang; Zhao, Gengyan; Bradshaw, Tyler; McMillan, Alan B

2018-05-15

In this study, we explore the feasibility of a novel framework for MR-based attenuation correction for PET/MR imaging based on deep learning via convolutional neural networks, which enables fully automated and robust estimation of a pseudo CT image based on ultrashort echo time (UTE), fat, and water images obtained by a rapid MR acquisition. MR images for MRAC are acquired using dual echo ramped hybrid encoding (dRHE), where both UTE and out-of-phase echo images are obtained within a short single acquisition (35 sec). Tissue labeling of air, soft tissue, and bone in the UTE image is accomplished via a deep learning network that was pre-trained with T1-weighted MR images. UTE images are used as input to the network, which was trained using labels derived from co-registered CT images. The tissue labels estimated by deep learning are refined by a conditional random field based correction. The soft tissue labels are further separated into fat and water components using the two-point Dixon method. The estimated bone, air, fat, and water images are then assigned appropriate Hounsfield units, resulting in a pseudo CT image for PET attenuation correction. To evaluate the proposed MRAC method, PET/MR imaging of the head was performed on 8 human subjects, where Dice similarity coefficients of the estimated tissue labels and relative PET errors were evaluated through comparison to a registered CT image. Dice coefficients for air (within the head), soft tissue, and bone labels were 0.76±0.03, 0.96±0.006, and 0.88±0.01. In PET quantification, the proposed MRAC method produced relative PET errors less than 1% within most brain regions. The proposed MRAC method utilizing deep learning with transfer learning and an efficient dRHE acquisition enables reliable PET quantification with accurate and rapid pseudo CT generation. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

BLAST Ring Image Generator (BRIG: simple prokaryote genome comparisons

Directory of Open Access Journals (Sweden)

Beatson Scott A

2011-08-01

Full Text Available Abstract Background Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. Results BLAST Ring Image Generator (BRIG can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.

Science.gov (United States)

Alikhan, Nabil-Fareed; Petty, Nicola K; Ben Zakour, Nouri L; Beatson, Scott A

2011-08-08

Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically. There is a clear need for a user

Applicability of the 3D-VIBE sequence to whole brain imaging

International Nuclear Information System (INIS)

Makabe, Takeshi; Nakamura, Manami; Moriyama, Ryo

2009-01-01

The volumetric interpolated breath-hold examination (VIBE) method has been developed imaging also holds its breath in an abdomen, and to do three-dimensional T1WI in possible time in gradient echo sequence, and applied to dynamic study mainly and planning for time reduction using an interpolation and partial fourier. We considered the condition for imaging to do whole brain as high resolution image using VIBE. Even if base matrix was maintained when an interpolation and partial fourier were used too much excessively by Phantom experiment, the resolution of multiplanar reconstruction (MPR) image fell. There was a limit of the interpolation therefore to maintain the resolution as voxel. Signal-to-noise ratio (SNR) fell by flip angle (FA) increase by the applicability to the head, and peak existed in about 15 deg in contrast-to-noise ratio (CNR) of white matter and gray matter. Therefore by it's clinical and optimizing the imaging condition of VIBE, whole brain, it was imaging possible in about 3 minutes as high resolution image. (author)

Comparison of modern 3D and 2D MR imaging sequences of the wrist at 3 Tesla

International Nuclear Information System (INIS)

Rehnitz, C.; Klaan, B.; Amarteifio, E.; Kauczor, H.U.; Weber, M.A.; Stillfried, F. von; Burkholder, I.

2016-01-01

To compare the image quality of modern 3 D and 2 D sequences for dedicated wrist imaging at 3 Tesla (T) MRI. At 3 T MRI, 18 patients (mean age: 36.2 years) with wrist pain and 16 healthy volunteers (mean age: 26.4 years) were examined using 2 D proton density-weighted fat-saturated (PDfs), isotropic 3 D TrueFISP, 3 D MEDIC, and 3 D PDfs SPACE sequences. Image quality was rated on a five-point scale (0 - 4) including overall image quality (OIQ), visibility of important structures (cartilage, ligaments, TFCC) and degree of artifacts. Signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) of cartilage/bone/muscle/fluid as well as the mean overall SNR/CNR were calculated using region-of-interest analysis. ANOVA, paired t-, and Wilcoxon-signed-rank tests were applied. The image quality of all tested sequences was superior to 3 D PDfs SPACE (p < 0.01). 3 D TrueFISP had the highest combined cartilage score (mean: 3.4) and performed better in cartilage comparisons against 3 D PDfs SPACE in both groups and 2 D PDfs in volunteers (p < 0.05). 3 D MEDIC performed better in 7 of 8 comparisons (p < 0.05) regarding ligaments and TFCC. 2 D PDfs provided constantly high scores. The mean overall SNR/CNR for 2 D PDfs, 3 D PDfs SPACE, 3 D TrueFISP, and 3 D MEDIC were 68/65, 32/27, 45/47, and 57/45, respectively. 2 D PDfs performed best in most SNR/CNR comparisons (p < 0.05) and 3 D MEDIC performed best within the 3 D sequences (p < 0.05). Except 3 D PDfs SPACE, all tested 3 D and 2 D sequences provided high image quality. 3 D TrueFISP was best for cartilage imaging, 3 D MEDIC for ligaments and TFCC and 2 D PDfs for general wrist imaging.

PETRA, MSVAT-SPACE and SEMAC sequences for metal artefact reduction in dental MR imaging

International Nuclear Information System (INIS)

Hilgenfeld, Tim; Heil, Alexander; Bendszus, Martin; Prager, Marcel; Heiland, Sabine; Schwindling, Franz Sebastian; Rammelsberg, Peter; Nittka, Mathias; Grodzki, David

2017-01-01

Dental MRI is often impaired by artefacts due to metallic dental materials. Several sequences were developed to reduce susceptibility artefacts. Here, we evaluated a set of sequences for artefact reduction for dental MRI for the first time. Artefact volume, signal-to-noise ratio (SNR) and image quality were assessed on a 3-T MRI for pointwise encoding time reduction with radial acquisition (PETRA), multiple-slab acquisition with view angle tilting gradient, based on a sampling perfection with application-optimised contrasts using different flip angle evolution (SPACE) sequence (MSVAT-SPACE), slice-encoding for metal-artefact correction (SEMAC) and compared to a standard SPACE and a standard turbo-spin-echo (TSE) sequence. Field-of-view and acquisition times were chosen to enable in vivo application. Two implant-supported prostheses were tested (porcelain fused to metal non-precious alloy and monolithic zirconia). Smallest artefact was measured for TSE sequences with no difference between the standard TSE and the SEMAC. MSVAT-SPACE reduced artefacts about 56% compared to the standard SPACE. Effect of the PETRA was dependent on sample used. Image quality and SNR were comparable for all sequences except PETRA, which yielded poor results. There is no benefit in terms of artefact reduction for SEMAC compared to standard TSE. Usage of MSVAT-SPACE is advantageous since artefacts are reduced and higher resolution is achieved. (orig.)

PETRA, MSVAT-SPACE and SEMAC sequences for metal artefact reduction in dental MR imaging

Energy Technology Data Exchange (ETDEWEB)

Hilgenfeld, Tim; Heil, Alexander; Bendszus, Martin [Heidelberg University Hospital, Department of Neuroradiology, Heidelberg (Germany); Prager, Marcel; Heiland, Sabine [Heidelberg University Hospital, Department of Neuroradiology, Heidelberg (Germany); Heidelberg University Hospital, Section of Experimental Radiology, Heidelberg (Germany); Schwindling, Franz Sebastian; Rammelsberg, Peter [Heidelberg University Hospital, Department of Prosthodontics, Heidelberg (Germany); Nittka, Mathias; Grodzki, David [Siemens Healthcare GmbH, Erlangen (Germany)

2017-12-15

Dental MRI is often impaired by artefacts due to metallic dental materials. Several sequences were developed to reduce susceptibility artefacts. Here, we evaluated a set of sequences for artefact reduction for dental MRI for the first time. Artefact volume, signal-to-noise ratio (SNR) and image quality were assessed on a 3-T MRI for pointwise encoding time reduction with radial acquisition (PETRA), multiple-slab acquisition with view angle tilting gradient, based on a sampling perfection with application-optimised contrasts using different flip angle evolution (SPACE) sequence (MSVAT-SPACE), slice-encoding for metal-artefact correction (SEMAC) and compared to a standard SPACE and a standard turbo-spin-echo (TSE) sequence. Field-of-view and acquisition times were chosen to enable in vivo application. Two implant-supported prostheses were tested (porcelain fused to metal non-precious alloy and monolithic zirconia). Smallest artefact was measured for TSE sequences with no difference between the standard TSE and the SEMAC. MSVAT-SPACE reduced artefacts about 56% compared to the standard SPACE. Effect of the PETRA was dependent on sample used. Image quality and SNR were comparable for all sequences except PETRA, which yielded poor results. There is no benefit in terms of artefact reduction for SEMAC compared to standard TSE. Usage of MSVAT-SPACE is advantageous since artefacts are reduced and higher resolution is achieved. (orig.)

Magnetic resonance visualization of conductive structures by sequence-triggered direct currents and spin-echo phase imaging

Energy Technology Data Exchange (ETDEWEB)

Eibofner, Frank; Wojtczyk, Hanne; Graf, Hansjörg, E-mail: hansjoerg.graf@med.uni-tuebingen.de, E-mail: drGraf@t-online.de [Section on Experimental Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany); Clasen, Stephan [Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany)

2014-06-15

Purpose: Instrument visualization in interventional magnetic resonance imaging (MRI) is commonly performed via susceptibility artifacts. Unfortunately, this approach suffers from limited conspicuity in inhomogeneous tissue and disturbed spatial encoding. Also, susceptibility artifacts are controllable only by sequence parameters. This work presents the basics of a new visualization method overcoming such problems by applying sequence-triggered direct current (DC) pulses in spin-echo (SE) imaging. SE phase images allow for background free current path localization. Methods: Application of a sequence-triggered DC pulse in SE imaging, e.g., during a time period between radiofrequency excitation and refocusing, results in transient field inhomogeneities. Dependent on the additional z-magnetic field from the DC, a phase offset results despite the refocusing pulse. False spatial encoding is avoided by DC application during periods when read-out or slice-encoding gradients are inactive. A water phantom containing a brass conductor (water equivalent susceptibility) and a titanium needle (serving as susceptibility source) was used to demonstrate the feasibility. Artifact dependence on current strength and orientation was examined. Results: Without DC, the brass conductor was only visible due to its water displacement. The titanium needle showed typical susceptibility artifacts. Applying triggered DC pulses, the phase offset of spins near the conductor appeared. Because SE phase images are homogenous also in regions of persistent field inhomogeneities, the position of the conductor could be determined with high reliability. Artifact characteristic could be easily controlled by amperage leaving sequence parameters unchanged. For an angle of 30° between current and static field visualization was still possible. Conclusions: SE phase images display the position of a conductor carrying pulsed DC free from artifacts caused by persistent field inhomogeneities. Magnitude and phase

Rapid identification of salmonella serotypes with stereo and hyperspectral microscope imaging Methods

Science.gov (United States)

The hyperspectral microscope imaging (HMI) method can reduce detection time within 8 hours including incubation process. The early and rapid detection with this method in conjunction with the high throughput capabilities makes HMI method a prime candidate for implementation for the food industry. Th...

Direct sequencing for rapid detection of multidrug resistant Mycobacterium tuberculosis strains in Morocco

Directory of Open Access Journals (Sweden)

Zakham F

2013-11-01

Full Text Available Fathiah Zakham,1,4 Imane Chaoui,1 Amina Hadbae Echchaoui,2 Fouad Chetioui,3 My Driss Elmessaoudi,3 My Mustapha Ennaji,4 Mohammed Abid,2 Mohammed El Mzibri11Unité de Biologie et Recherché Médicale, Centre National de l'Energie, des Sciences et des Techniques Nucléaires (CNESTEN, Rabat, 2Laboratoire de Génétique Mycobacterienne, Institut Pasteur, Tangier, 3Laboratoire de Tuberculose Institut Pasteur, Casablanca, 4Laboratoire de Microbiologie, Hygiène et Virologie, Faculté des Sciences et Techniques, Mohammedia, MoroccoBackground: Tuberculosis (TB is a major public health problem with high mortality and morbidity rates, especially in low-income countries. Disturbingly, the emergence of multidrug resistant (MDR and extensively drug resistant (XDR TB cases has worsened the situation, raising concerns of a future epidemic of virtually untreatable TB. Indeed, the rapid diagnosis of MDR TB is a critical issue for TB management. This study is an attempt to establish a rapid diagnosis of MDR TB by sequencing the target fragments of the rpoB gene which linked to resistance against rifampicin and the katG gene and inhA promoter region, which are associated with resistance to isoniazid.Methods: For this purpose, 133 sputum samples of TB patients from Morocco were enrolled in this study. One hundred samples were collected from new cases, and the remaining 33 were from previously treated patients (drug relapse or failure, chronic cases and did not respond to anti-TB drugs after a sufficient duration of treatment. All samples were subjected to rpoB, katG and pinhA mutation analysis by polymerase chain reaction and DNA sequencing.Results: Molecular analysis showed that seven strains were isoniazid-monoresistant and 17 were rifampicin-monoresistant. MDR TB strains were identified in nine cases (6.8%. Among them, eight were traditionally diagnosed as critical cases, comprising four chronic and four drug-relapse cases. The last strain was isolated from a

Gadobenate dimeglumine-enhanced MR of VX2 carcinoma in rabbit liver: usefulness of the delayed phase imaging and optimal pulse sequence

Energy Technology Data Exchange (ETDEWEB)

Cho, Seung Il; Lee, Jeong Min; Kim, Young Kon; Kim, Chong Soo [College of Medicine, Chonbuk National Univ., Chonju (Korea, Republic of)

2002-07-01

To assess the diagnostic value of delayed imaging using gadobenate dimeglumine (MultiHance) and to determine the optimal pulse sequence for the detection of VX2 carcinoma lesions in the rabbit. Twelve VX2 carcinomas implanted in the livers of eleven New Zealand rabbits were studied. All patients underwent an MR protocal consisting of precontrast T2-and T1-weighted sequences, followed by repetition of the T1-weighted sequence at 0 to 30 (arterial phase). 31-60 (portal phase), and 40 minutes (delayed phase) after the intravenous administration of 0.1 mmol/kg of gadobenate dimeglumine. The signal-to-noise ratio (SNR) of the liver and VX2 tumor, and the lesion-to-liver contrast-to-noise ratio (CNR) of precontrast and postcontrast MR images were quantitatively analyzed, and two experienced radiologists evaluated image quality in terms of lesion conspicuity, artifact, mass delineation, and vascular anatomy. Liver SNR was significantly higher at delayed imaging than at precontrast, arterial, and portal imaging (p<0.05), while lesion SNR was significantly higher at delayed imaging than at precontrast imaging (p<0.05). Lesion CNR was higher at delayed imaging than at precontrast and portal phase imaging (p<0.05), but there was no difference between arterial and delayed imaging. The latter provided better mass delineation than precontrast, arterial and portal phase imaging (p<0.05). While in terms of lesion conspicuity and vascular anatomy, the delayed phase was better than the arterial phase (p<0.05) but similar to the precontrast and portal phase. During the delayed phase, the gradient-echo sequence showed better results than the spin-echo in terms of liver SNR, and lesion SNR and CNR (p<0.05). Because it provides better lesion conspicuity and mass delineation by improving liver SNR and lesion-to-liver CNR, the addition of the delayed phase to a dynamic MRI sequence after gadobenate dimeglumine adminstration facilitates lesion detection. For delayed-phase imaging, the

Gadobenate dimeglumine-enhanced MR of VX2 carcinoma in rabbit liver: usefulness of the delayed phase imaging and optimal pulse sequence

International Nuclear Information System (INIS)

Cho, Seung Il; Lee, Jeong Min; Kim, Young Kon; Kim, Chong Soo

2002-01-01

To assess the diagnostic value of delayed imaging using gadobenate dimeglumine (MultiHance) and to determine the optimal pulse sequence for the detection of VX2 carcinoma lesions in the rabbit. Twelve VX2 carcinomas implanted in the livers of eleven New Zealand rabbits were studied. All patients underwent an MR protocal consisting of precontrast T2-and T1-weighted sequences, followed by repetition of the T1-weighted sequence at 0 to 30 (arterial phase). 31-60 (portal phase), and 40 minutes (delayed phase) after the intravenous administration of 0.1 mmol/kg of gadobenate dimeglumine. The signal-to-noise ratio (SNR) of the liver and VX2 tumor, and the lesion-to-liver contrast-to-noise ratio (CNR) of precontrast and postcontrast MR images were quantitatively analyzed, and two experienced radiologists evaluated image quality in terms of lesion conspicuity, artifact, mass delineation, and vascular anatomy. Liver SNR was significantly higher at delayed imaging than at precontrast, arterial, and portal imaging (p<0.05), while lesion SNR was significantly higher at delayed imaging than at precontrast imaging (p<0.05). Lesion CNR was higher at delayed imaging than at precontrast and portal phase imaging (p<0.05), but there was no difference between arterial and delayed imaging. The latter provided better mass delineation than precontrast, arterial and portal phase imaging (p<0.05). While in terms of lesion conspicuity and vascular anatomy, the delayed phase was better than the arterial phase (p<0.05) but similar to the precontrast and portal phase. During the delayed phase, the gradient-echo sequence showed better results than the spin-echo in terms of liver SNR, and lesion SNR and CNR (p<0.05). Because it provides better lesion conspicuity and mass delineation by improving liver SNR and lesion-to-liver CNR, the addition of the delayed phase to a dynamic MRI sequence after gadobenate dimeglumine adminstration facilitates lesion detection. For delayed-phase imaging, the

Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues.

Science.gov (United States)

Wang, Yu; Woehrstein, Johannes B; Donoghue, Noah; Dai, Mingjie; Avendaño, Maier S; Schackmann, Ron C J; Zoeller, Jason J; Wang, Shan Shan H; Tillberg, Paul W; Park, Demian; Lapan, Sylvain W; Boyden, Edward S; Brugge, Joan S; Kaeser, Pascal S; Church, George M; Agasti, Sarit S; Jungmann, Ralf; Yin, Peng

2017-10-11

To decipher the molecular mechanisms of biological function, it is critical to map the molecular composition of individual cells or even more importantly tissue samples in the context of their biological environment in situ. Immunofluorescence (IF) provides specific labeling for molecular profiling. However, conventional IF methods have finite multiplexing capabilities due to spectral overlap of the fluorophores. Various sequential imaging methods have been developed to circumvent this spectral limit but are not widely adopted due to the common limitation of requiring multirounds of slow (typically over 2 h at room temperature to overnight at 4 °C in practice) immunostaining. We present here a practical and robust method, which we call DNA Exchange Imaging (DEI), for rapid in situ spectrally unlimited multiplexing. This technique overcomes speed restrictions by allowing for single-round immunostaining with DNA-barcoded antibodies, followed by rapid (less than 10 min) buffer exchange of fluorophore-bearing DNA imager strands. The programmability of DEI allows us to apply it to diverse microscopy platforms (with Exchange Confocal, Exchange-SIM, Exchange-STED, and Exchange-PAINT demonstrated here) at multiple desired resolution scales (from ∼300 nm down to sub-20 nm). We optimized and validated the use of DEI in complex biological samples, including primary neuron cultures and tissue sections. These results collectively suggest DNA exchange as a versatile, practical platform for rapid, highly multiplexed in situ imaging, potentially enabling new applications ranging from basic science, to drug discovery, and to clinical pathology.

Diffusion tensor imaging. Theory, sequence optimization and application in Alzheimer's disease

International Nuclear Information System (INIS)

Stieltjes, B.; Schlueter, M.; Hahn, H.K.; Wilhelm, T.; Essig, M.

2003-01-01

Diffusion tensor imaging (DTI) offers an in vivo view into the microarchitecture of the brain. Furthermore it allows a three-dimensional reconstruction of fiber tracts. We will discuss the principles of DTI and possibilities for sequence optimization. Finally we will give an overview of DTI and its application in Alzheimer's disease. (orig.) [de

Evaluation of Magnetic Resonance Imaging-Compatible Needles and Interactive Sequences for Musculoskeletal Interventions Using an Open High-Field Magnetic Resonance Imaging Scanner

International Nuclear Information System (INIS)

Wonneberger, Uta; Schnackenburg, Bernhard; Streitparth, Florian; Walter, Thula; Rump, Jens; Teichgraeber, Ulf K. M.

2010-01-01

In this article, we study in vitro evaluation of needle artefacts and image quality for musculoskeletal laser-interventions in an open high-field magnetic resonance imaging (MRI) scanner at 1.0T with vertical field orientation. Five commercially available MRI-compatible puncture needles were assessed based on artefact characteristics in a CuSO4 phantom (0.1%) and in human cadaveric lumbar spines. First, six different interventional sequences were evaluated with varying needle orientation to the main magnetic field B0 (0 o to 90 o ) in a sequence test. Artefact width, needle-tip error, and contrast-to-noise ratio (CNR) were calculated. Second, a gradient-echo sequence used for thermometric monitoring was assessed and in varying echo times, artefact width, tip error, and signal-to-noise ratio (SNR) were measured. Artefact width and needle-tip error correlated with needle material, instrument orientation to B0, and sequence type. Fast spin-echo sequences produced the smallest needle artefacts for all needles, except for the carbon fibre needle (width o to B0. Overall, the proton density-weighted spin-echo sequences had the best CNR (CNR Muscle/Needle >16.8). Concerning the thermometric gradient echo sequence, artefacts remained <5 mm, and the SNR reached its maximum at an echo time of 15 ms. If needle materials and sequences are accordingly combined, guidance and monitoring of musculoskeletal laser interventions may be feasible in a vertical magnetic field at 1.0T.

Automatic registration of panoramic image sequence and mobile laser scanning data using semantic features

Science.gov (United States)

Li, Jianping; Yang, Bisheng; Chen, Chi; Huang, Ronggang; Dong, Zhen; Xiao, Wen

2018-02-01

Inaccurate exterior orientation parameters (EoPs) between sensors obtained by pre-calibration leads to failure of registration between panoramic image sequence and mobile laser scanning data. To address this challenge, this paper proposes an automatic registration method based on semantic features extracted from panoramic images and point clouds. Firstly, accurate rotation parameters between the panoramic camera and the laser scanner are estimated using GPS and IMU aided structure from motion (SfM). The initial EoPs of panoramic images are obtained at the same time. Secondly, vehicles in panoramic images are extracted by the Faster-RCNN as candidate primitives to be matched with potential corresponding primitives in point clouds according to the initial EoPs. Finally, translation between the panoramic camera and the laser scanner is refined by maximizing the overlapping area of corresponding primitive pairs based on the Particle Swarm Optimization (PSO), resulting in a finer registration between panoramic image sequences and point clouds. Two challenging urban scenes were experimented to assess the proposed method, and the final registration errors of these two scenes were both less than three pixels, which demonstrates a high level of automation, robustness and accuracy.

Minimization of Dead-Periods in MRI Pulse Sequences for Imaging Oblique Planes

Science.gov (United States)

Atalar, Ergin; McVeigh, Elliot R.

2007-01-01

With the advent of breath-hold MR cardiac imaging techniques, the minimization of TR and TE for oblique planes has become a critical issue. The slew rates and maximum currents of gradient amplifiers limit the minimum possible TR and TE by adding dead-periods to the pulse sequences. We propose a method of designing gradient waveforms that will be applied to the amplifiers instead of the slice, readout, and phase encoding waveforms. Because this method ensures that the gradient amplifiers will always switch at their maximum slew rate, it results in the minimum possible dead-period for given imaging parameters and scan plane position. A GRASS pulse sequence has been designed and ultra-short TR and TE values have been obtained with standard gradient amplifiers and coils. For some oblique slices, we have achieved shorter TR and TE values than those for nonoblique slices. PMID:7869900

An Extended Multilocus Sequence Typing (MLST Scheme for Rapid Direct Typing of Leptospira from Clinical Samples.

Directory of Open Access Journals (Sweden)

Sabrina Weiss

2016-09-01

Full Text Available Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST data direct from patient specimens while minimising costs for subsequent sequencing.An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen types from patients diagnosed with leptospirosis between 2014 and 2015 in the United Kingdom (UK and the Lao Peoples Democratic Republic (Lao PDR. Of 44 clinical samples (23 serum, 6 whole blood, 3 buffy coat, 12 urine PCR positive for pathogenic Leptospira spp. at least one allele was amplified in 22 samples (50% and used for phylogenetic inference. Full allelic profiles were obtained from ten specimens, representing all sample types (23%. No nonspecific amplicons were observed in any of the samples. Of twelve PCR positive urine specimens three gave full allelic profiles (25% and two a partial profile. Phylogenetic analysis allowed for species assignment. The predominant species detected was L. interrogans (10/14 and 7/8 from UK and Lao PDR, respectively. All other species were detected in samples from only one country (Lao PDR: L. borgpetersenii [1/8]; UK: L. kirschneri [1/14], L. santarosai [1/14], L. weilii [2/14].Typing information of pathogenic Leptospira spp. was obtained directly from a variety of clinical samples using a modified MLST assay. This assay negates the need for time-consuming culture of Leptospira prior to typing and will be of use both in surveillance, as single alleles enable species determination, and outbreaks for the rapid identification of clusters.

Rapid prototyping of biomimetic vascular phantoms for hyperspectral reflectance imaging

Science.gov (United States)

Ghassemi, Pejhman; Wang, Jianting; Melchiorri, Anthony J.; Ramella-Roman, Jessica C.; Mathews, Scott A.; Coburn, James C.; Sorg, Brian S.; Chen, Yu; Joshua Pfefer, T.

2015-12-01

The emerging technique of rapid prototyping with three-dimensional (3-D) printers provides a simple yet revolutionary method for fabricating objects with arbitrary geometry. The use of 3-D printing for generating morphologically biomimetic tissue phantoms based on medical images represents a potentially major advance over existing phantom approaches. Toward the goal of image-defined phantoms, we converted a segmented fundus image of the human retina into a matrix format and edited it to achieve a geometry suitable for printing. Phantoms with vessel-simulating channels were then printed using a photoreactive resin providing biologically relevant turbidity, as determined by spectrophotometry. The morphology of printed vessels was validated by x-ray microcomputed tomography. Channels were filled with hemoglobin (Hb) solutions undergoing desaturation, and phantoms were imaged with a near-infrared hyperspectral reflectance imaging system. Additionally, a phantom was printed incorporating two disjoint vascular networks at different depths, each filled with Hb solutions at different saturation levels. Light propagation effects noted during these measurements-including the influence of vessel density and depth on Hb concentration and saturation estimates, and the effect of wavelength on vessel visualization depth-were evaluated. Overall, our findings indicated that 3-D-printed biomimetic phantoms hold significant potential as realistic and practical tools for elucidating light-tissue interactions and characterizing biophotonic system performance.

The Optimization of Magnetic Resonance Imaging Pulse Sequences in Order to Better Detection of Multiple Sclerosis Plaques.

Science.gov (United States)

Farshidfar, Z; Faeghi, F; Haghighatkhah, H R; Abdolmohammadi, J

2017-09-01

Magnetic resonance imaging (MRI) is the most sensitive technique to detect multiple sclerosis (MS) plaques in central nervous system. In some cases, the patients who were suspected to MS, Whereas MRI images are normal, but whether patients don't have MS plaques or MRI images are not enough optimized enough in order to show MS plaques? The aim of the current study is evaluating the efficiency of different MRI sequences in order to better detection of MS plaques. In this cross-sectional study which was performed at Shohada-E Tajrish in Tehran - Iran hospital between October, 2011 to April, 2012, included 20 patients who suspected to MS disease were selected by the method of random sampling and underwent routine brain Pulse sequences (Axial T2w, Axial T1w, Coronal T2w, Sagittal T1w, Axial FLAIR) by Siemens, Avanto, 1.5 Tesla system. If any lesion which is suspected to the MS disease was observed, additional sequences such as: Sagittal FLAIR Fat Sat, Sagittal PDw-fat Sat, Sagittal PDw-water sat was also performed. This study was performed in about 52 lesions and the results in more than 19 lesions showed that, for the Subcortical and Infratentorial areas, PDWw sequence with fat suppression is the best choice, And in nearly 33 plaques located in Periventricular area, FLAIR Fat Sat was the most effective sequence than both PDw fat and water suppression pulse sequences. Although large plaques may visible in all images, but important problem in patients with suspected MS is screening the tiny MS plaques. This study showed that for revealing the MS plaques located in the Subcortical and Infratentorial areas, PDw-fat sat is the most effective sequence, and for MS plaques in the periventricular area, FLAIR fat Sat is the best choice.

Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus

Science.gov (United States)

Hughes, Joseph; Biek, Roman; Litster, Annette; Willett, Brian J.; Hosie, Margaret J.

2015-01-01

Analysing the evolution of feline immunodeficiency virus (FIV) at the intra-host level is important in order to address whether the diversity and composition of viral quasispecies affect disease progression. We examined the intra-host diversity and the evolutionary rates of the entire env and structural fragments of the env sequences obtained from sequential blood samples in 43 naturally infected domestic cats that displayed different clinical outcomes. We observed in the majority of cats that FIV env showed very low levels of intra-host diversity. We estimated that env evolved at a rate of 1.16×10−3 substitutions per site per year and demonstrated that recombinant sequences evolved faster than non-recombinant sequences. It was evident that the V3–V5 fragment of FIV env displayed higher evolutionary rates in healthy cats than in those with terminal illness. Our study provided the first evidence that the leader sequence of env, rather than the V3–V5 sequence, had the highest intra-host diversity and the highest evolutionary rate of all env fragments, consistent with this region being under a strong selective pressure for genetic variation. Overall, FIV env displayed relatively low intra-host diversity and evolved slowly in naturally infected cats. The maximum evolutionary rate was observed in the leader sequence of env. Although genetic stability is not necessarily a prerequisite for clinical stability, the higher genetic stability of FIV compared with human immunodeficiency virus might explain why many naturally infected cats do not progress rapidly to AIDS. PMID:25535323

Superresolution restoration of an image sequence: adaptive filtering approach.

Science.gov (United States)

Elad, M; Feuer, A

1999-01-01

This paper presents a new method based on adaptive filtering theory for superresolution restoration of continuous image sequences. The proposed methodology suggests least squares (LS) estimators which adapt in time, based on adaptive filters, least mean squares (LMS) or recursive least squares (RLS). The adaptation enables the treatment of linear space and time-variant blurring and arbitrary motion, both of them assumed known. The proposed new approach is shown to be of relatively low computational requirements. Simulations demonstrating the superresolution restoration algorithms are presented.

A method of rapidly evaluating image quality of NED optical system

Science.gov (United States)

Sun, Qi; Qiu, Chuankai; Yang, Huan

2014-11-01

In recent years, with the development of technology of micro-display, advanced optics and the software and hardware, near-to-eye display ( NED) optical system will have a wide range of potential applications in the fields of amusement and virtual reality. However, research on the evaluating image quality of this kind optical system is comparatively lagging behind. Although now there are some methods and equipment for evaluation, they can't be applied in commercial production because of their complex operation and inaccuracy. In this paper, an academic method is proposed and a Rapid Evaluation System (RES) is designed to evaluate the image of optical system rapidly and exactly. Firstly, a set of parameters that eyes are sensitive to and also express the quality of system should be extracted and quantized to be criterion, so the evaluation standards can be established. Then, some parameters can be detected by RES consisted of micro-display, CCD camera and computer and so on. By process of scaling, the measuring results of the RES are exact and creditable, relationship between object measurement, subjective evaluation and the RES will be established. After that, image quality of optical system can be evaluated just by detecting parameters of that. The RES is simple and the results of evaluation are exact and keeping with human vision. So the method can be used not only for optimizing design of optical system, but also for evaluation in commercial production.

In vivo quantitative NMR imaging of fruit tissues during growth using Spoiled Gradient Echo sequence

DEFF Research Database (Denmark)

Kenouche, S.; Perrier, M.; Bertin, N.

2014-01-01

of this study was to design a robust and accurate quantitative measurement method based on NMR imaging combined with contrast agent (CA) for mapping and quantifying water transport in growing cherry tomato fruits. A multiple flip-angle Spoiled Gradient Echo (SGE) imaging sequence was used to evaluate...

An objective method to optimize the MR sequence set for plaque classification in carotid vessel wall images using automated image segmentation.

Directory of Open Access Journals (Sweden)

Ronald van 't Klooster

Full Text Available A typical MR imaging protocol to study the status of atherosclerosis in the carotid artery consists of the application of multiple MR sequences. Since scanner time is limited, a balance has to be reached between the duration of the applied MR protocol and the quantity and quality of the resulting images which are needed to assess the disease. In this study an objective method to optimize the MR sequence set for classification of soft plaque in vessel wall images of the carotid artery using automated image segmentation was developed. The automated method employs statistical pattern recognition techniques and was developed based on an extensive set of MR contrast weightings and corresponding manual segmentations of the vessel wall and soft plaque components, which were validated by histological sections. Evaluation of the results from nine contrast weightings showed the tradeoff between scan duration and automated image segmentation performance. For our dataset the best segmentation performance was achieved by selecting five contrast weightings. Similar performance was achieved with a set of three contrast weightings, which resulted in a reduction of scan time by more than 60%. The presented approach can help others to optimize MR imaging protocols by investigating the tradeoff between scan duration and automated image segmentation performance possibly leading to shorter scanning times and better image interpretation. This approach can potentially also be applied to other research fields focusing on different diseases and anatomical regions.

Optic disc boundary segmentation from diffeomorphic demons registration of monocular fundus image sequences versus 3D visualization of stereo fundus image pairs for automated early stage glaucoma assessment

Science.gov (United States)

Gatti, Vijay; Hill, Jason; Mitra, Sunanda; Nutter, Brian

2014-03-01

Despite the current availability in resource-rich regions of advanced technologies in scanning and 3-D imaging in current ophthalmology practice, world-wide screening tests for early detection and progression of glaucoma still consist of a variety of simple tools, including fundus image-based parameters such as CDR (cup to disc diameter ratio) and CAR (cup to disc area ratio), especially in resource -poor regions. Reliable automated computation of the relevant parameters from fundus image sequences requires robust non-rigid registration and segmentation techniques. Recent research work demonstrated that proper non-rigid registration of multi-view monocular fundus image sequences could result in acceptable segmentation of cup boundaries for automated computation of CAR and CDR. This research work introduces a composite diffeomorphic demons registration algorithm for segmentation of cup boundaries from a sequence of monocular images and compares the resulting CAR and CDR values with those computed manually by experts and from 3-D visualization of stereo pairs. Our preliminary results show that the automated computation of CDR and CAR from composite diffeomorphic segmentation of monocular image sequences yield values comparable with those from the other two techniques and thus may provide global healthcare with a cost-effective yet accurate tool for management of glaucoma in its early stage.

Water imaging (hydrography) in the fetus: the value of a heavily T2-weighted sequence

Energy Technology Data Exchange (ETDEWEB)

Kline-Fath, Beth M.; Calvo-Garcia, Maria A.; O' Hara, Sara M.; Racadio, Judy M. [University of Cincinnati Medical Center, Department of Radiology, Cincinnati Children' s Hospital Medical Center, Cincinnati, OH (United States)

2007-02-15

Since the development of fast imaging sequences, MR has proved to be a helpful tool in the evaluation of fetal pathology. Because of the high water content of fetal tissues and pathology, hydrography imaging (MR fetography) can provide additional diagnostic information. To demonstrate the benefit of MR fetography in fetal imaging. From 2004 to 2005, 126 fetal MR examinations were performed for evaluation of an abnormality depicted on an antenatal sonogram. Single-shot fast spin-echo MR imaging and MR fetography were performed through the area of fetal pathology. The two studies were retrospectively compared. The primary diagnosis was not changed with the addition of MR fetography. New findings, particularly in the kidneys and spine, were identified in 9% of the patients. When fetal pathology was of high water content (80% patients), the MR fetography imaging increased diagnostic confidence. In 11% of the patients, those with cardiovascular or low water pathology, the MR fetography was not beneficial. The mainstay of fetal imaging is currently the HASTE and SSFSE sequences. However, MR fetography is an excellent adjunct that highlights fetal pathology by reinforcing the diagnosis, identifying additional findings, and providing high-contrast high-resolution images that are helpful when counseling clinicians and patients. (orig.)

Hybrid PET/MR imaging: an algorithm to reduce metal artifacts from dental implants in Dixon-based attenuation map generation using a multiacquisition variable-resonance image combination sequence.

Science.gov (United States)

Burger, Irene A; Wurnig, Moritz C; Becker, Anton S; Kenkel, David; Delso, Gaspar; Veit-Haibach, Patrick; Boss, Andreas

2015-01-01

It was the aim of this study to implement an algorithm modifying Dixon-based MR imaging datasets for attenuation correction in hybrid PET/MR imaging with a multiacquisition variable resonance image combination (MAVRIC) sequence to reduce metal artifacts. After ethics approval, in 8 oncologic patients with dental implants data were acquired in a trimodality setup with PET/CT and MR imaging. The protocol included a whole-body 3-dimensional dual gradient-echo sequence (Dixon) used for MR imaging-based PET attenuation correction and a high-resolution MAVRIC sequence, applied in the oral area compromised by dental implants. An algorithm was implemented correcting the Dixon-based μ maps using the MAVRIC in areas of Dixon signal voids. The artifact size of the corrected μ maps was compared with the uncorrected MR imaging μ maps. The algorithm was robust in all patients. There was a significant reduction in mean artifact size of 70.5% between uncorrected and corrected μ maps from 697 ± 589 mm(2) to 202 ± 119 mm(2) (P = 0.016). The proposed algorithm could improve MR imaging-based attenuation correction in critical areas, when standard attenuation correction is hampered by metal artifacts, using a MAVRIC. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

MRI of the cartilages of the knee, 3-D imaging with a rapid computer system

Energy Technology Data Exchange (ETDEWEB)

Adam, G.; Bohndorf, K.; Prescher, A.; Drobnitzky, M.; Guenther, R.W.

1989-01-01

2-D spin-echo sequences were compared with 3-D gradient-echo sequences using normal and cadaver knee joints. The important advantages of 3-D-imaging are: sections of less than 1 mm, reconstruction in any required plane, which can be related to the complex anatomy of the knee joint, and very good distinction between intra-articular fluid, fibrocartilage and hyaline cartilage. (orig./GDG).

Impact of Rocuronium and Succinylcholine on Sedation Initiation After Rapid Sequence Intubation.

Science.gov (United States)

Johnson, Eric G; Meier, Alex; Shirakbari, Alicia; Weant, Kyle; Baker Justice, Stephanie

2015-07-01

Rapid sequence intubation (RSI) involves a rapidly acting sedative plus a neuromuscular blocking agent (NMBA) to facilitate endotracheal intubation. Rocuronium and succinylcholine are NMBAs commonly used in RSI with drastically different durations of action. Evaluate whether patients receiving RSI with a longer-acting NMBA had a greater delay in sedation or analgesia than patients that received a short-acting NMBA. This was a retrospective review of patients presenting to the emergency department requiring endotracheal intubation. Exclusions included age rocuronium or succinylcholine. Secondary endpoints included hospital length of stay (HLOS), intensive care unit length of stay (ICU LOS), and impact of an emergency medicine pharmacist (EPh). A total 106 patients met inclusion criteria, 76 patients receiving rocuronium and 30 receiving succinylcholine. Mean time to sedation or analgesia was longer in the rocuronium group when compared to the succinylcholine group at 34 ± 36 min vs. 16 ± 21 min (p = 0.002). In the presence of an EPh, the mean time to sedation or analgesia was 20 ± 21 min, vs. 49 ± 45 min (p rocuronium in RSI had a significantly longer time to sedation or analgesia when compared to patients receiving succinylcholine. The presence of an EPh significantly decreased the time to administration of sedation or analgesia after RSI. Copyright © 2015 Elsevier Inc. All rights reserved.

The value of MR imaging of PDFASAT sequence in the diagnosis of extremities occult fractures

International Nuclear Information System (INIS)

Lu Lingquan; Xu Mingshen; Wu Qianzhi; Mao Chunnan; Wang Shuzi; Zhou Xingfan; Wang Liping

2004-01-01

Objective: To investigate the value of MR imaging of proton density weighted-fat saturated (PDFASAT) sequence in detecting the occult fracture of extremities. Methods: Thirty-one patients with acute trauma were studied using radiography and MR imaging within 45 days. MR sequences included FSE T 1 WI, T 2 WI, and PDFASAT. 21 occult fractures occurred in the knee joint, 6 in the hip joint, 1 in the elbow joint, 2 in the shoulder, and 1 in the ankle. Results: All 31 cases had normal radiographic results. 10 cases with proximal fibula, 4 with proximal tibia and 7 with femur condyle occult fractures were found in 21 knee joint acute trauma cases. 2 cases with intertrochanteric, 2 with femoral neck and 2 with cotyle occult fractures were found in 6 hip joint trauma cases. 2 proximal humerus occult fractures were found in 2 shoulder cases. 1 distal humerus and 1 distal fibula occult fracture was found in elbow and ankle cases. MR imaging demonstrated irregular linear low signal in the subcortical region on both T 1 WI and T 2 WI, and high signal changes around low signal were seen on T 2 WI in some cases. The high signal in PDFASAT sequence was more remarkable and wider than that on both T 1 WI and T 2 WI. Conclusion: MR imaging could determine the diagnosis of acute and chronic occult fractures. MRI should be the next choice when plain films fail to reveal suspected fractures in setting of suggestive symptoms and positive physical examination. PDFASAT would be the best effective sequence among the T 1 WI, T 2 WI, and PDFASAT. (author)

Ultra-fast low-angle rapid acquisition and relaxation enhancement (UFLARE) in patients with epilepsy

International Nuclear Information System (INIS)

Eriksson, S.H.; Symms, M.R.; Woermann, F.G.; Kendall, B.; Stevens, J.M.; Stepney, A.; Barker, G.J.; Niendorf, T.

2001-01-01

MRI is an important diagnostic tool in patients with epilepsy, but patient motion during long scans may result in image artefacts. We studied the utility of an ultra-fast MR sequence in patients with epilepsy. Ultra-fast low-angle rapid acquisition and relaxation enhancement (UFLARE) images were acquired for 100 consecutive patients and nine control subjects. Scans were compared with routine T2-weighted spin echo images for signal-to-noise ratio, contrast, and conspicuity, followed by a blind review of lesion detectability. UFLARE scans were also acquired for 15 patients who moved during conventional scans. All UFLARE scans had lower signal-to-noise ratios and lower contrast than the T2-weighted images. Compared with T1- and T2-weighted, PD and FLAIR images, 86% of hippocampal sclerosis (HS), 92% of large but only 24% of small white-matter lesions were detected on the blind review of the UFLARE images. Reduced motion artefacts were seen on the UFLARE images in all 15 patients who moved during the conventional scans, and in three patients UFLARE was the only sequence we were able to obtain. Despite the lower lesion detectability for smaller lesions, the use of an ultra-fast MRI sequence such as UFLARE may be very useful in patients who are not able to co-operate during conventional MRI examinations, if a general anaesthetic is to be avoided. (orig.)

Rapid prototyping of biomimetic vascular phantoms for hyperspectral reflectance imaging

Science.gov (United States)

Ghassemi, Pejhman; Wang, Jianting; Melchiorri, Anthony J.; Ramella-Roman, Jessica C.; Mathews, Scott A.; Coburn, James C.; Sorg, Brian S.; Chen, Yu; Joshua Pfefer, T.

2015-01-01

Abstract. The emerging technique of rapid prototyping with three-dimensional (3-D) printers provides a simple yet revolutionary method for fabricating objects with arbitrary geometry. The use of 3-D printing for generating morphologically biomimetic tissue phantoms based on medical images represents a potentially major advance over existing phantom approaches. Toward the goal of image-defined phantoms, we converted a segmented fundus image of the human retina into a matrix format and edited it to achieve a geometry suitable for printing. Phantoms with vessel-simulating channels were then printed using a photoreactive resin providing biologically relevant turbidity, as determined by spectrophotometry. The morphology of printed vessels was validated by x-ray microcomputed tomography. Channels were filled with hemoglobin (Hb) solutions undergoing desaturation, and phantoms were imaged with a near-infrared hyperspectral reflectance imaging system. Additionally, a phantom was printed incorporating two disjoint vascular networks at different depths, each filled with Hb solutions at different saturation levels. Light propagation effects noted during these measurements—including the influence of vessel density and depth on Hb concentration and saturation estimates, and the effect of wavelength on vessel visualization depth—were evaluated. Overall, our findings indicated that 3-D-printed biomimetic phantoms hold significant potential as realistic and practical tools for elucidating light–tissue interactions and characterizing biophotonic system performance. PMID:26662064

Imaging 2015 Mw 7.8 Gorkha Earthquake and Its Aftershock Sequence Combining Multiple Calibrated Global Seismic Arrays

Science.gov (United States)

LI, B.; Ghosh, A.

2016-12-01

The 2015 Mw 7.8 Gorkha earthquake provides a good opportunity to study the tectonics and earthquake hazards in the Himalayas, one of the most seismically active plate boundaries. Details of the seismicity patterns and associated structures in the Himalayas are poorly understood mainly due to limited instrumentation. Here, we apply a back-projection method to study the mainshock rupture and the following aftershock sequence using four large aperture global seismic arrays. All the arrays show eastward rupture propagation of about 130 km and reveal similar evolution of seismic energy radiation, with strong high-frequency energy burst about 50 km north of Kathmandu. Each single array, however, is typically limited by large azimuthal gap, low resolution, and artifacts due to unmodeled velocity structures. Therefore, we use a self-consistent empirical calibration method to combine four different arrays to image the Gorkha event. It greatly improves the resolution, can better track rupture and reveal details that cannot be resolved by any individual array. In addition, we also use the same arrays at teleseismic distances and apply a back-projection technique to detect and locate the aftershocks immediately following the Gorkha earthquake. We detect about 2.5 times the aftershocks recorded by the Advance National Seismic System comprehensive earthquake catalog during the 19 days following the mainshock. The aftershocks detected by the arrays show an east-west trend in general, with majority of the aftershocks located at the eastern part of the rupture patch and surrounding the rupture zone of the largest Mw 7.3 aftershock. Overall spatiotemporal aftershock pattern agrees well with global catalog, with our catalog showing more details relative to the standard global catalog. The improved aftershock catalog enables us to better study the aftershock dynamics, stress evolution in this region. Moreover, rapid and better imaging of aftershock distribution may aid rapid response

Fast ultrasonic imaging in a liquid filled pipe

International Nuclear Information System (INIS)

Kolbe, W.F.; Turko, B.T.; Leskovar, B.

1985-10-01

A new method is described for the imaging of the interior of a liquid filled metallic pipe using acoustical techniques. The experimental system incorporates an array of 20 acoustical transducers and is capable of capturing the images of moving bubbles at a frame rate in excess of 300/s. The transducers are mounted circumferentially around the pipe. Each transducer is pulsed in sequence, and the echoes reflected from vapor bubbles in the interior are detected, digitized and processed by a computer to generate an image. The high rate of speed was achieved by the use of newly developed software and electronic circuitry. This approach has eliminated most of the spurious echo signals which degraded the performance of previous imaging systems. The capability of the method is illustrated by imaging actual vapor bubbles in rapid sequence in the pipe. 13 refs

Magnetic nanoparticle imaging by random and maximum length sequences of inhomogeneous activation fields.

Science.gov (United States)

Baumgarten, Daniel; Eichardt, Roland; Crevecoeur, Guillaume; Supriyanto, Eko; Haueisen, Jens

2013-01-01

Biomedical applications of magnetic nanoparticles require a precise knowledge of their biodistribution. From multi-channel magnetorelaxometry measurements, this distribution can be determined by means of inverse methods. It was recently shown that the combination of sequential inhomogeneous excitation fields in these measurements is favorable regarding the reconstruction accuracy when compared to homogeneous activation . In this paper, approaches for the determination of activation sequences for these measurements are investigated. Therefor, consecutive activation of single coils, random activation patterns and families of m-sequences are examined in computer simulations involving a sample measurement setup and compared with respect to the relative condition number of the system matrix. We obtain that the values of this condition number decrease with larger number of measurement samples for all approaches. Random sequences and m-sequences reveal similar results with a significant reduction of the required number of samples. We conclude that the application of pseudo-random sequences for sequential activation in the magnetorelaxometry imaging of magnetic nanoparticles considerably reduces the number of required sequences while preserving the relevant measurement information.

Holistic and component plant phenotyping using temporal image sequence.

Science.gov (United States)

Das Choudhury, Sruti; Bashyam, Srinidhi; Qiu, Yumou; Samal, Ashok; Awada, Tala

2018-01-01

Image-based plant phenotyping facilitates the extraction of traits noninvasively by analyzing large number of plants in a relatively short period of time. It has the potential to compute advanced phenotypes by considering the whole plant as a single object (holistic phenotypes) or as individual components, i.e., leaves and the stem (component phenotypes), to investigate the biophysical characteristics of the plants. The emergence timing, total number of leaves present at any point of time and the growth of individual leaves during vegetative stage life cycle of the maize plants are significant phenotypic expressions that best contribute to assess the plant vigor. However, image-based automated solution to this novel problem is yet to be explored. A set of new holistic and component phenotypes are introduced in this paper. To compute the component phenotypes, it is essential to detect the individual leaves and the stem. Thus, the paper introduces a novel method to reliably detect the leaves and the stem of the maize plants by analyzing 2-dimensional visible light image sequences captured from the side using a graph based approach. The total number of leaves are counted and the length of each leaf is measured for all images in the sequence to monitor leaf growth. To evaluate the performance of the proposed algorithm, we introduce University of Nebraska-Lincoln Component Plant Phenotyping Dataset (UNL-CPPD) and provide ground truth to facilitate new algorithm development and uniform comparison. The temporal variation of the component phenotypes regulated by genotypes and environment (i.e., greenhouse) are experimentally demonstrated for the maize plants on UNL-CPPD. Statistical models are applied to analyze the greenhouse environment impact and demonstrate the genetic regulation of the temporal variation of the holistic phenotypes on the public dataset called Panicoid Phenomap-1. The central contribution of the paper is a novel computer vision based algorithm for

Method for automatic localization of MR-visible markers using morphological image processing and conventional pulse sequences: feasibility for image-guided procedures.

Science.gov (United States)

Busse, Harald; Trampel, Robert; Gründer, Wilfried; Moche, Michael; Kahn, Thomas

2007-10-01

To evaluate the feasibility and accuracy of an automated method to determine the 3D position of MR-visible markers. Inductively coupled RF coils were imaged in a whole-body 1.5T scanner using the body coil and two conventional gradient echo sequences (FLASH and TrueFISP) and large imaging volumes up to (300 mm(3)). To minimize background signals, a flip angle of approximately 1 degrees was used. Morphological 2D image processing in orthogonal scan planes was used to determine the 3D positions of a configuration of three fiducial markers (FMC). The accuracies of the marker positions and of the orientation of the plane defined by the FMC were evaluated at various distances r(M) from the isocenter. Fiducial marker detection with conventional equipment (pulse sequences, imaging coils) was very reliable and highly reproducible over a wide range of experimental conditions. For r(M) image processing is feasible, simple, and very accurate. In combination with safe wireless markers, the method is found to be useful for image-guided procedures. (c) 2007 Wiley-Liss, Inc.

Basic concepts from magnetic resonance imaging

International Nuclear Information System (INIS)

Rodriguez Arroyo, Diego

2011-01-01

The use of magnetic resonance imaging (MRI) has grown exponentially, due in part to excellent anatomic and pathologic detail provided by the modality, as recent technological advances that have led to more rapid acquisition times. Radiology residents in different parts of the world now receive training in MR images from their first year of residence, included the pulse sequences training spin-echo, gradient-echo, inversion-recovery, echo-planar image and MR angiographic sequences, commonly used in medical imaging. However, to optimize the use of this type of study, it has been necessary to understand the basic concepts of physics, included the concepts of recovery T1, degradation T2* and T2, repetition time, echo time, and the effects of chemical shift. Additionally, it has been important to understand the contrast weighting for better representation of specific tissues and thus perform an appropriate differential diagnosis of various pathological processes. (author) [es

Fast ultrasonic imaging in a liquid filled pipe

International Nuclear Information System (INIS)

Kolbe, W.F.; Turko, B.T.; Leskovar, B.

1986-01-01

A new method is described for the imaging of the interior of a liquid filled metallic pipe using acoustical techniques. The experimental system incorporates an array of 20 acoustical transducers and is capable of capturing the images of moving bubbles at a frame rate in excess of 300/s. The transducers are mounted circumferentially around the pipe. Each transducer is pulsed in sequence, and the echoes reflected from vapor bubbles in the interior are detected, digitized and processed by a computer to generate an image. The high rate of speed was achieved by the use of newly developed software and electronic circuitry. This approach has eliminated most of the spurious echo signals which degraded the performance of previous imaging systems. The capability of the method is illustrated by imaging actual vapor bubbles in rapid sequence in the pipe. The described imaging system is used to examine reactor cooling systems

Imaging techniques and investigation protocols in pediatric emergency imaging

International Nuclear Information System (INIS)

Scharitzer, M.; Hoermann, M.; Puig, S.; Prokop, M.

2002-01-01

Paediatric emergencies demand a quick and efficient radiological investigation with special attention to specific adjustments related to patient age and radiation protection. Imaging modalities are improving rapidly and enable to diagnose childhood diseases and injuries more quickly, accurately and safely. This article provides an overview of imaging techniques adjusted to the age of the child and an overview of imaging strategies of common paediatric emergencies. Optimising the imaging parameters (digital radiography, different screen-film systems, exposure specifications) allows for substantial reduction of radiation dose. Spiral- and multislice-CT reduce scan time and enable a considerable reduction of radiation exposure if scanning parameters (pitch setting, tube current) are properly adjusted. MRI is still mainly used for neurological or spinal emergencies despite the advent of fast imaging sequences. The radiologist's task is to select an appropriate imaging strategy according to expected differential diagnosis and to adjust the imaging techniques to the individual patient. (orig.) [de

A generative Bezier curve model for surf-zone tracking in coastal image sequences

CSIR Research Space (South Africa)

Burke, Michael G

2017-09-01

Full Text Available This work introduces a generative Bezier curve model suitable for surf-zone curve tracking in coastal image sequences. The model combines an adaptive curve parametrised by control points governed by local random walks with a global sinusoidal motion...

Assessment of relevant hepatic steatosis in obese adolescents by rapid fat-selective GRE imaging with spatial-spectral excitation: a quantitative comparison with spectroscopic findings

International Nuclear Information System (INIS)

Springer, Fabian; Schick, Fritz; Ehehalt, Stefan; Binder, Gerhard; Sommer, Julia; Ballweg, Verena; Machann, Juergen; Claussen, Claus D.

2011-01-01

To test the feasibility of fat-selective GRE imaging using a spectral-spatial excitation technique for determination of intrahepatic lipid content (IHL) in obese adolescents. Fat-selective MR imaging (1.5 T) was applied to record a single axial slice through a representative liver region within a single breath-hold. The sequence uses six equidistant slice-selective excitation pulses with binomial amplitude ratios to achieve high selectivity for lipid signals after appropriate shimming. IHL MRI content was quantified using signal intensity of adjacent subcutaneous adipose tissue. As the gold standard for IHL quantification, single-voxel stimulated echo magnetic resonance spectroscopy (MRS) was applied. IHL MRS was quantified using the water peak as a reference. Forty-five MR examinations could be performed, and IHL MRS content ranged from 0.7% to 19.1%. Results from MRS and fat-selective imaging correlated well with Spearman coefficients between r = 0.78 and r = 0.86. There were no relevant regional differences in IHL within the liver parenchyma (p > 0.6359). Fat-selective imaging was able to reliably identify patients with IHL content above 5% with positive/negative likelihood ratio of 11.8 and 0.05, respectively. Fat-selective MR imaging provides both a reliable and a convenient method of rapidly quantifying IHL content in obese adolescents. (orig.)

DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures

OpenAIRE

Thomson, John P.; Fawkes, Angie; Ottaviano, Raffaele; Hunter, Jennifer M.; Shukla, Ruchi; Mjoseng, Heidi K.; Clark, Richard; Coutts, Audrey; Murphy, Lee; Meehan, Richard R.

2015-01-01

Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially ...

Clinical application of three dimensional ultrafast MR imaging to intracerebral traumatic lesions

International Nuclear Information System (INIS)

Enomoto, Kyoko; Amanuma, Makoto; Hasegawa, Makoto; Watabe, Tsuneya; Heshiki, Atsuko

1994-01-01

We applied a T1-weighted three-dimensional (3D) magnetization-prepared rapid gradient-echo sequence (MPRAGE) for the detection of intracerebral lesions associated with closed head injuries. Thirty-four patients underwent brain MR imaging on a 1.5 Tesla superconducting MR unit. We applied an MPRAGE sequence, together with spin echo (SE) and gradient echo (GRE) sequences, and evaluated the detectability of lesions with each sequence. A total of 100 intracerebral traumatic lesions (33 cortical contusion, 56 diffuse axonal injury, 11 subcortical gray matter injury) were found. Ninety-seven percent of all lesions were detected on MPRAGE images, and 67% on SE and GRE images. The detectability of lesions in each category was 91%, 98%, and 100% on MPRAGE images, and 88%, 54%, and 73% on either SE or GRE images. 3D MPRAGE is a promising method to detect intracerebral traumatic lesions, particularly those associated with diffuse axonal injury, because of its high quality of contrast and spatial resolution and the capability of image reconstruction in any plane. (author)

EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures.

Science.gov (United States)

Reynolds, Christopher R; Islam, Suhail A; Sternberg, Michael J E

2018-01-31

EzMol is a molecular visualization Web server in the form of a software wizard, located at http://www.sbg.bio.ic.ac.uk/ezmol/. It is designed for easy and rapid image manipulation and display of protein molecules, and is intended for users who need to quickly produce high-resolution images of protein molecules but do not have the time or inclination to use a software molecular visualization system. EzMol allows the upload of molecular structure files in PDB format to generate a Web page including a representation of the structure that the user can manipulate. EzMol provides intuitive options for chain display, adjusting the color/transparency of residues, side chains and protein surfaces, and for adding labels to residues. The final adjusted protein image can then be downloaded as a high-resolution image. There are a range of applications for rapid protein display, including the illustration of specific areas of a protein structure and the rapid prototyping of images. Copyright © 2018. Published by Elsevier Ltd.

Ultrafast T2-weighted single shot spin-echo sequences: applications on abdominal and pelvic pathologies

International Nuclear Information System (INIS)

Martin, J.; Martin, C.; Falco, J.; Esteban, L.

1999-01-01

The magnetic resonance imaging (MRI) sequences that obtain all the data using a sole excitation pulse of 90 degree centigrade, filling the K space in a single repetition time (TR) is known as snap shot or single shot (SS). The SS sequence based on the rapid acquisition with relaxation enhancement (SS-RARE) method, designed by Hening (1) and a variation of it with a half-Fourier reconstruction (SS-HF-RARE (HASTEL)) (2, 3) are capable of obtaining high contrast images in T2, in very short times, that oscillate between one to several seconds. The clinical application of these sequences to abdominal and pelvic pathologies is increasing, providing and improvement in the contrast resolution, but also in the spatial resolution, with a high relation signal/noise ratio, high contrast and absence of movement artifacts. (Author)

Common crus aplasia: diagnosis by 3D volume rendering imaging using 3DFT-CISS sequence

International Nuclear Information System (INIS)

Kim, H.J.; Song, J.W.; Chon, K.-M.; Goh, E.-K.

2004-01-01

AIM: The purpose of this study was to evaluate the findings of three-dimensional (3D) volume rendering (VR) imaging in common crus aplasia (CCA) of the inner ear. MATERIALS AND METHODS: Using 3D VR imaging of temporal bone constructive interference in steady state (CISS) magnetic resonance (MR) images, we retrospectively reviewed seven inner ears of six children who were candidates for cochlear implants and who had been diagnosed with CCA. As controls, we used the same method to examine 402 inner ears of 201 patients who had no clinical symptoms or signs of sensorineural hearing loss. Temporal bone MR imaging (MRI) was performed with a 1.5 T MR machine using a CISS sequence, and VR of the inner ear was performed on a work station. Morphological image analysis was performed on rotation views of 3D VR images. RESULTS: In all seven cases, CCA was diagnosed by the absence of the common crus. The remaining superior semicircular canal (SCC) was normal in five and hypoplastic in two inner ears, while the posterior SCC was normal in all seven. One patient showed bilateral symmetrical CCA. Complicated combined anomalies were seen in the cochlea, vestibule and lateral SCC. CONCLUSION: 3D VR imaging findings with MR CISS sequence can directly diagnose CCA. This technique may be useful in delineating detailed anomalies of SCCs

Mapping soil heterogeneity using RapidEye satellite images

Science.gov (United States)

Piccard, Isabelle; Eerens, Herman; Dong, Qinghan; Gobin, Anne; Goffart, Jean-Pierre; Curnel, Yannick; Planchon, Viviane

2016-04-01

In the frame of BELCAM, a project funded by the Belgian Science Policy Office (BELSPO), researchers from UCL, ULg, CRA-W and VITO aim to set up a collaborative system to develop and deliver relevant information for agricultural monitoring in Belgium. The main objective is to develop remote sensing methods and processing chains able to ingest crowd sourcing data, provided by farmers or associated partners, and to deliver in return relevant and up-to-date information for crop monitoring at the field and district level based on Sentinel-1 and -2 satellite imagery. One of the developments within BELCAM concerns an automatic procedure to detect soil heterogeneity within a parcel using optical high resolution images. Such heterogeneity maps can be used to adjust farming practices according to the detected heterogeneity. This heterogeneity may for instance be caused by differences in mineral composition of the soil, organic matter content, soil moisture or soil texture. Local differences in plant growth may be indicative for differences in soil characteristics. As such remote sensing derived vegetation indices may be used to reveal soil heterogeneity. VITO started to delineate homogeneous zones within parcels by analyzing a series of RapidEye images acquired in 2015 (as a precursor for Sentinel-2). Both unsupervised classification (ISODATA, K-means) and segmentation techniques were tested. Heterogeneity maps were generated from images acquired at different moments during the season (13 May, 30 June, 17 July, 31 August, 11 September and 1 November 2015). Tests were performed using blue, green, red, red edge and NIR reflectances separately and using derived indices such as NDVI, fAPAR, CIrededge, NDRE2. The results for selected winter wheat, maize and potato fields were evaluated together with experts from the collaborating agricultural research centers. For a few fields UAV images and/or yield measurements were available for comparison.

Noninvasive imaging of three-dimensional cardiac activation sequence during pacing and ventricular tachycardia.

Science.gov (United States)

Han, Chengzong; Pogwizd, Steven M; Killingsworth, Cheryl R; He, Bin

2011-08-01

Imaging cardiac excitation within ventricular myocardium is important in the treatment of cardiac arrhythmias and might help improve our understanding of arrhythmia mechanisms. This study sought to rigorously assess the imaging performance of a 3-dimensional (3D) cardiac electrical imaging (3DCEI) technique with the aid of 3D intracardiac mapping from up to 216 intramural sites during paced rhythm and norepinephrine (NE)-induced ventricular tachycardia (VT) in the rabbit heart. Body surface potentials and intramural bipolar electrical recordings were simultaneously measured in a closed-chest condition in 13 healthy rabbits. Single-site pacing and dual-site pacing were performed from ventricular walls and septum. VTs and premature ventricular complexes (PVCs) were induced by intravenous NE. Computed tomography images were obtained to construct geometry models. The noninvasively imaged activation sequence correlated well with invasively measured counterpart, with a correlation coefficient of 0.72 ± 0.04, and a relative error of 0.30 ± 0.02 averaged over 520 paced beats as well as 73 NE-induced PVCs and VT beats. All PVCs and VT beats initiated in the subendocardium by a nonreentrant mechanism. The averaged distance from the imaged site of initial activation to the pacing site or site of arrhythmias determined from intracardiac mapping was ∼5 mm. For dual-site pacing, the double origins were identified when they were located at contralateral sides of ventricles or at the lateral wall and the apex. 3DCEI can noninvasively delineate important features of focal or multifocal ventricular excitation. It offers the potential to aid in localizing the origins and imaging activation sequences of ventricular arrhythmias, and to provide noninvasive assessment of the underlying arrhythmia mechanisms. Copyright © 2011 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Magnetic resonance imaging: effects of magnetic field strength

International Nuclear Information System (INIS)

Crooks, L.E.; Arakawa, M.; Hoenninger, J.; McCarten, B.; Watts, J.; Kaufman, L.

1984-01-01

Magnetic resonance images of the head, abdomen, and pelvis of normal adult men were obtained using varying magnetic field strength, and measurements of T1 and T2 relaxations and of signal-to-noise (SN) ratios were determined. For any one spin echo sequence, gray/white matter contrast decreases and muscle/fat contrast increases with field. SN levels rise rapidly up to 3.0 kgauss and then change more slowly, actually dropping for muscle. The optimum field for magnetic resonance imaging depends on tissue type, body part, and imaging sequence, so that it does not have a unique value. Magnetic resonance systems that operate in the 3.0-5.0 kgauss range achieve most or all of the gains that can be achieved by higher magnetic fields

Rapid visuomotor processing of phobic images in spider- and snake-fearful participants.

Science.gov (United States)

Haberkamp, Anke; Schmidt, Filipp; Schmidt, Thomas

2013-10-01

This study investigates enhanced visuomotor processing of phobic compared to fear-relevant and neutral stimuli. We used a response priming design to measure rapid, automatic motor activation by natural images (spiders, snakes, mushrooms, and flowers) in spider-fearful, snake-fearful, and control participants. We found strong priming effects in all tasks and conditions; however, results showed marked differences between groups. Most importantly, in the group of spider-fearful individuals, spider pictures had a strong and specific influence on even the fastest motor responses: Phobic primes entailed the largest priming effects, and phobic targets accelerated responses, both effects indicating speeded response activation by phobic images. In snake-fearful participants, this processing enhancement for phobic material was less pronounced and extended to both snake and spider images. We conclude that spider phobia leads to enhanced processing capacity for phobic images. We argue that this is enabled by long-term perceptual learning processes. © 2013.

Sequence assembly

DEFF Research Database (Denmark)

Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

2009-01-01

Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

The processing of images of biological threats in visual short-term memory.

Science.gov (United States)

Quinlan, Philip T; Yue, Yue; Cohen, Dale J

2017-08-30

The idea that there is enhanced memory for negatively, emotionally charged pictures was examined. Performance was measured under rapid, serial visual presentation (RSVP) conditions in which, on every trial, a sequence of six photo-images was presented. Briefly after the offset of the sequence, two alternative images (a target and a foil) were presented and participants attempted to choose which image had occurred in the sequence. Images were of threatening and non-threatening cats and dogs. The target depicted either an animal expressing an emotion distinct from the other images, or the sequences contained only images depicting the same emotional valence. Enhanced memory was found for targets that differed in emotional valence from the other sequence images, compared to targets that expressed the same emotional valence. Further controls in stimulus selection were then introduced and the same emotional distinctiveness effect obtained. In ruling out possible visual and attentional accounts of the data, an informal dual route topic model is discussed. This places emphasis on how visual short-term memory reveals a sensitivity to the emotional content of the input as it unfolds over time. Items that present with a distinctive emotional content stand out in memory. © 2017 The Author(s).

Effects of imaging gradients in sequences with varying longitudinal storage time-Case of diffusion exchange imaging.

Science.gov (United States)

Lasič, Samo; Lundell, Henrik; Topgaard, Daniel; Dyrby, Tim B

2018-04-01

To illustrate the potential bias caused by imaging gradients in correlation MRI sequences using longitudinal magnetization storage (LS) and examine the case of filter exchange imaging (FEXI) yielding maps of the apparent exchange rate (AXR). The effects of imaging gradients in FEXI were observed on yeast cells. To analyze the AXR bias, signal evolution was calculated by applying matrix exponential operators. A sharp threshold for the slice thickness was identified, below which the AXR is increasingly underestimated. The bias can be understood in terms of an extended low-pass diffusion filtering during the LS interval, which is more pronounced at lower exchange rates. For a total exchange rate constant larger than 1 s -1 , the AXR bias is expected to be negligible when slices thicker than 2.5 mm are used. In correlation experiments like FEXI, relying on LS with variable duration, imaging gradients may cause disrupting effects that cannot be easily mitigated and should be carefully considered for unbiased results. In typical clinical applications of FEXI, the imaging gradients are expected to cause a negligible AXR bias. However, the AXR bias may be significant in preclinical settings or whenever thin imaging slices are used. Magn Reson Med 79:2228-2235, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Driven equilibrium (drive) MR imaging of the cranial nerves V-VIII: comparison with the T2-weighted 3D TSE sequence

Energy Technology Data Exchange (ETDEWEB)

Ciftci, E. E-mail: eciftcis7@hotmail.com; Anik, Yonca; Arslan, Arzu; Akansel, Gur; Sarisoy, Tahsin; Demirci, Ali

2004-09-01

Purpose: The aim of this study is to evaluate the efficacy of the driven equilibrium radio frequency reset pulse (DRIVE) on image quality and nerve detection when used in adjunction with T2-weighted 3D turbo spin-echo (TSE) sequence. Materials and methods: Forty-five patients with cranial nerve symptoms referable to the cerebellopontine angle (CPA) were examined using a T2-weighted 3D TSE pulse sequence with and without DRIVE. MR imaging was performed on a 1.5-T MRI scanner. In addition to the axial resource images, reformatted oblique sagittal, oblique coronal and maximum intensity projection (MIP) images of the inner ear were evaluated. The nerve identification and image quality were graded for the cranial nerves V-VIII as well as inner ear structures. These structures were chosen because fluid-solid interfaces existed due to the CSF around (the cranial nerves V-VIII) or the endolymph within (the inner ear structures). Statistical analysis was performed using the Wilcoxon test. P<0.05 was considered significant. Results: The addition of the DRIVE pulse shortens the scan time by 25%. T2-weighted 3D TSE sequence with DRIVE performed slightly better than the T2-weighted 3D TSE sequence without DRIVE in identifying the individual nerves. The image quality was also slightly better with DRIVE. Conclusion: The addition of the DRIVE pulse to the T2-weighted 3D TSE sequence is preferable when imaging the cranial nerves surrounded by the CSF, or fluid-filled structures because of shorter scan time and better image quality due to reduced flow artifacts.

Driven equilibrium (drive) MR imaging of the cranial nerves V-VIII: comparison with the T2-weighted 3D TSE sequence

International Nuclear Information System (INIS)

Ciftci, E.; Anik, Yonca; Arslan, Arzu; Akansel, Gur; Sarisoy, Tahsin; Demirci, Ali

2004-01-01

Purpose: The aim of this study is to evaluate the efficacy of the driven equilibrium radio frequency reset pulse (DRIVE) on image quality and nerve detection when used in adjunction with T2-weighted 3D turbo spin-echo (TSE) sequence. Materials and methods: Forty-five patients with cranial nerve symptoms referable to the cerebellopontine angle (CPA) were examined using a T2-weighted 3D TSE pulse sequence with and without DRIVE. MR imaging was performed on a 1.5-T MRI scanner. In addition to the axial resource images, reformatted oblique sagittal, oblique coronal and maximum intensity projection (MIP) images of the inner ear were evaluated. The nerve identification and image quality were graded for the cranial nerves V-VIII as well as inner ear structures. These structures were chosen because fluid-solid interfaces existed due to the CSF around (the cranial nerves V-VIII) or the endolymph within (the inner ear structures). Statistical analysis was performed using the Wilcoxon test. P<0.05 was considered significant. Results: The addition of the DRIVE pulse shortens the scan time by 25%. T2-weighted 3D TSE sequence with DRIVE performed slightly better than the T2-weighted 3D TSE sequence without DRIVE in identifying the individual nerves. The image quality was also slightly better with DRIVE. Conclusion: The addition of the DRIVE pulse to the T2-weighted 3D TSE sequence is preferable when imaging the cranial nerves surrounded by the CSF, or fluid-filled structures because of shorter scan time and better image quality due to reduced flow artifacts

The rapid secondary electron imaging system of the proton beam writer at CIBA

International Nuclear Information System (INIS)

Udalagama, C.N.B.; Bettiol, A.A.; Kan, J.A. van; Teo, E.J.; Watt, F.

2007-01-01

The recent years have witnessed a proliferation of research involving proton beam (p-beam) writing. This has prompted investigations into means of optimizing the process of p-beam writing so as to make it less time consuming and more efficient. One such avenue is the improvement of the pre-writing preparatory procedures that involves beam focusing and sample alignment which is centred on acquiring images of a resolution standard or sample. The conventional mode of imaging used up to now has utilized conventional nuclear microprobe signals that are of a pulsed nature and are inherently slow. In this work, we report the new imaging system that has been introduced, which uses proton induced secondary electrons. This in conjunction with software developed in-house that uses a National Instruments DAQ card with hardware triggering, facilitates large data transfer rates enabling rapid imaging. Frame rates as much as 10 frames/s have been achieved at an imaging resolution of 512 x 512 pixels

Gadolinium-enhanced MR imaging of normal renal transplants. An evaluation of a T1-weighted dynamic echo-planar sequence

International Nuclear Information System (INIS)

Dupas, B.; Blancho, G.; Havet, T.; Leaute, F.

1999-01-01

Purpose: To evaluate the potential usefulness of dynamic MR with echoplanar imaging (EPI) in assessing the renal function in patients with renal allografts. Material and methods: Using a T1-weighted sequence, EPI was performed after injection of a Gd-chelate in 17 patients with normally functioning renal allografts. Time-intensity curves were plotted from the signal intensity (SI) measurements of the cortex and the medulla. Results: The pattern of corticomedullar differentiation (CMD) observed after constrast enhancement was divided into four phases using the T1-EPI. After a rapid decrease in the SI of cortical structures, and a subsequent return to precontrast levels, a gradual fall in the SI of the medulla was observed. The average time between the two periods of signal loss was 60 s. Conclusion: This study illustrated the potential use of dynamic T1-EPI to demonstrate contrast-induced CMD in renal allografts. (orig.)

Rapid characterization of a nanomaterial structure using X-ray reciprocal-lattice-space imaging

International Nuclear Information System (INIS)

Sakata, Osami; Yoshimoto, Mamoru; Miki, Kazushi

2006-01-01

The X-ray reciprocal-lattice-space imaging method is able to record the reciprocal-lattice-space of nanostructure by sample-and-detector fixed geometry. This method was developed by the surface structure analysis beam line BL13XU of SPring-8. Outline of the X-ray diffraction method and basic principles of the X-ray reciprocal-lattice-space imaging method, and application examples are stated. The method is able to find out the Bragg conditions of nanostructure of surface in the atmosphere. The reciprocal-lattice of the embedded trace atomic wires was observed. The trace atoms of Bi atomic wires embedded in silicone showed the diffraction signal and image by a short exposure time. This method is useful at rapid non-destructive measurement of nanostructure. (S.Y.)

MRI investigation of normal fetal lung maturation using signal intensities on different imaging sequences

International Nuclear Information System (INIS)

Balassy, Csilla; Kasprian, Gregor; Weber, Michael; Hoermann, Marcus; Prayer, Daniela; Brugger, Peter C.; Csapo, Bence; Mittermayer, Christoph

2007-01-01

To purpose of this paper is to study the relation between normal lung maturation signal and changes in intensity ratios (SIR) and to determine which magnetic resonance imaging sequence provides the strongest correlation of normal lung SIs with gestational age. 126 normal singleton pregnancies (20-37 weeks) were examined with a 1.5 Tesla unit. Mean SIs for lungs, liver, and gastric fluid were assessed on six different sequences, and SIRs of lung/liver (LLSIR) and lung/gastric fluid (LGSIR) were correlated with gestational age for each sequence. To evaluate the feasibility of SIRs in the prediction of the state of the lung maturity, accuracy of the predicted SIRs (D*) was measured by calculating relative residuals (D*-D)/D for each sequence. LLSIRs showed significant changes in every sequence (p<0.05), while LGSIRs only on two sequences. Significant differences were shown for the mean of absolute residuals for both LLSIRs (p<0.001) and for LGSIRs (p=0.003). Relative residuals of LLSIRs were significantly smaller on T1-weighted sequence, whereas they were significantly higher for LGSIRs on FLAIR sequence. Fetal liver seems to be adequate reference for the investigation of lung maturation. T1-weighted sequence was the most accurate for the measurement of the lung SIs; thus, we propose to determine LLSIR on T1-weighted sequence when evaluating lung development. (orig.)

MRI investigation of normal fetal lung maturation using signal intensities on different imaging sequences

Energy Technology Data Exchange (ETDEWEB)

Balassy, Csilla; Kasprian, Gregor; Weber, Michael; Hoermann, Marcus; Prayer, Daniela [Medical University of Vienna, Department of Radiology, Vienna (Austria); Brugger, Peter C. [Medical University of Vienna, Center of Anatomy and Cell Biology, Vienna (Austria); Csapo, Bence [Medical University of Vienna, Department of Obstetrics and Gyneocology, Vienna (Austria); Mittermayer, Christoph [Medical University of Vienna, Department of Pediatrics, Vienna (Austria)

2007-03-15

To purpose of this paper is to study the relation between normal lung maturation signal and changes in intensity ratios (SIR) and to determine which magnetic resonance imaging sequence provides the strongest correlation of normal lung SIs with gestational age. 126 normal singleton pregnancies (20-37 weeks) were examined with a 1.5 Tesla unit. Mean SIs for lungs, liver, and gastric fluid were assessed on six different sequences, and SIRs of lung/liver (LLSIR) and lung/gastric fluid (LGSIR) were correlated with gestational age for each sequence. To evaluate the feasibility of SIRs in the prediction of the state of the lung maturity, accuracy of the predicted SIRs (D*) was measured by calculating relative residuals (D*-D)/D for each sequence. LLSIRs showed significant changes in every sequence (p<0.05), while LGSIRs only on two sequences. Significant differences were shown for the mean of absolute residuals for both LLSIRs (p<0.001) and for LGSIRs (p=0.003). Relative residuals of LLSIRs were significantly smaller on T1-weighted sequence, whereas they were significantly higher for LGSIRs on FLAIR sequence. Fetal liver seems to be adequate reference for the investigation of lung maturation. T1-weighted sequence was the most accurate for the measurement of the lung SIs; thus, we propose to determine LLSIR on T1-weighted sequence when evaluating lung development. (orig.)

Magnetic resonance urography in pediatrics: utilization of ultrafast single-shot spin echo sequences

International Nuclear Information System (INIS)

Martin, C.; Martin, J.; Duran, C.; Rigol, S.; Rojo, J. C.

1999-01-01

To determine the value of magnetic resonance urography (MRU) using ultrafast single-shot (SS) rapid acquisition with relaxation enhancement (RARE) and half-Fourier (HF) SS-RARE (SS-HF-RARE or HASTE) in the evaluation of congenital urinary tract anomalies in pediatric patients, and their possible application as alternatives to intravenous urography (IVU). Eighteen children (11 boys and 7 girls) aged 2 months to 15 years (mean: 5 years) with a total of 19 congenital urinary tract anomalies were studies by MU using SS-RARE and HASTE sequences in a 1 Tesla scanner. All the patients had previously been studies by ultrasound (US) and IVU. Twelve patients required anesthesia. The images were acquired by means of a HASTE sequence with multisection technique (TR, infinite; TE e f, 87 msec; echo train, 128; interval between echoes, 10.9 msec; total acquisition time, 13 sections/12 seconds), and SS-RARE (TR, infinite; TE e f, 1.100 msec; echo train, 240, and acquisition time, 7 seconds). Four radiologists evaluated the images independently; two who reviewed the IV images in consensus and two who reviewed the MRU images in consensus. The images were evaluated to assess the dilatation of the urinary tract and their utility in detecting the level and cause of the obstruction. MRU images revealed the urinary tract dilation, the level of the obstruction and the type of anomaly in 18 patients (100%), while IVU provided this information in only 10 [ sensitivity, 53%, 95% confidence interval (29%, 76%)]. The mean time required for MRU was 20 minutes (range: 7 to 30 minutes), while that of IVU was 1,242 minutes (range: 45 to 1,440 minutes). MRU using ultrafast single-short spin echo sequences is a rapid and effective technique that permits and excellent evaluation of congenital urinary tract anomalies in pediatric patients and does not require the administration of contrast media or ionizing radiation. (Author) 10 refs

Coil concepts for rapid and motion-compensated MR-Imaging of small animals

International Nuclear Information System (INIS)

Korn, Matthias

2009-01-01

In this work radiofrequency-coils for the imaging of small animals in clinical whole-body MRI-systems were developed. Therefore in a first step single-channel solenoids were designed and characterized. The solenoids had two and three windings respectively, which were implemented as double wires to increase the homogeneity of the receive profile. These coils allow the acquisition of whole-body images of mice with high signal-to-noise ratio and homogeneity over a distance of at least 6.3 cm. Since many imaging experiments require rapid image acquisition, in the next step a novel coil concept was developed, which, due to its geometry, enables parallel imaging in arbitrary directions. A prototype was assembled and tested on phantom and small-animal experiments. With an accelerating factor of R=2, the difference of the SNR in all directions from the theoretical maximum, was less than 1%. In order to compensate physiological motion by the self-gating technique, in this work a coil is presented for the first time, which selectively amplifies the self-gating signal, while - due to a optical detuning technique - preserving the homogeneous illumination of the image. In vivo experiments on a small animal show an amplification of the self-gating signal by at least 40%. (orig.)

Assessment of relevant hepatic steatosis in obese adolescents by rapid fat-selective GRE imaging with spatial-spectral excitation: a quantitative comparison with spectroscopic findings

Energy Technology Data Exchange (ETDEWEB)

Springer, Fabian; Schick, Fritz [University Hospital Tuebingen, Section on Experimental Radiology, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany); University Hospital Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany); Ehehalt, Stefan; Binder, Gerhard [University Children' s Hospital Tuebingen, Paediatric Endocrinology and Diabetes, Tuebingen (Germany); Sommer, Julia; Ballweg, Verena; Machann, Juergen [University Hospital Tuebingen, Section on Experimental Radiology, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany); Claussen, Claus D. [University Hospital Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany)

2011-04-15

To test the feasibility of fat-selective GRE imaging using a spectral-spatial excitation technique for determination of intrahepatic lipid content (IHL) in obese adolescents. Fat-selective MR imaging (1.5 T) was applied to record a single axial slice through a representative liver region within a single breath-hold. The sequence uses six equidistant slice-selective excitation pulses with binomial amplitude ratios to achieve high selectivity for lipid signals after appropriate shimming. IHL{sub MRI} content was quantified using signal intensity of adjacent subcutaneous adipose tissue. As the gold standard for IHL quantification, single-voxel stimulated echo magnetic resonance spectroscopy (MRS) was applied. IHL{sub MRS} was quantified using the water peak as a reference. Forty-five MR examinations could be performed, and IHL{sub MRS} content ranged from 0.7% to 19.1%. Results from MRS and fat-selective imaging correlated well with Spearman coefficients between r = 0.78 and r = 0.86. There were no relevant regional differences in IHL within the liver parenchyma (p > 0.6359). Fat-selective imaging was able to reliably identify patients with IHL content above 5% with positive/negative likelihood ratio of 11.8 and 0.05, respectively. Fat-selective MR imaging provides both a reliable and a convenient method of rapidly quantifying IHL content in obese adolescents. (orig.)

A Case Series of Rapid Prototyping and Intraoperative Imaging in Orbital Reconstruction

Science.gov (United States)

Lim, Christopher G.T.; Campbell, Duncan I.; Cook, Nicholas; Erasmus, Jason

2014-01-01

In Christchurch Hospital, rapid prototyping (RP) and intraoperative imaging are the standard of care in orbital trauma and has been used since February 2013. RP allows the fabrication of an anatomical model to visualize complex anatomical structures which is dimensionally accurate and cost effective. This assists diagnosis, planning, and preoperative implant adaptation for orbital reconstruction. Intraoperative imaging involves a computed tomography scan during surgery to evaluate surgical implants and restored anatomy and allows the clinician to correct errors in implant positioning that may occur during the same procedure. This article aims to demonstrate the potential clinical and cost saving benefits when both these technologies are used in orbital reconstruction which minimize the need for revision surgery. PMID:26000080

A case series of rapid prototyping and intraoperative imaging in orbital reconstruction.

Science.gov (United States)

Lim, Christopher G T; Campbell, Duncan I; Cook, Nicholas; Erasmus, Jason

2015-06-01

In Christchurch Hospital, rapid prototyping (RP) and intraoperative imaging are the standard of care in orbital trauma and has been used since February 2013. RP allows the fabrication of an anatomical model to visualize complex anatomical structures which is dimensionally accurate and cost effective. This assists diagnosis, planning, and preoperative implant adaptation for orbital reconstruction. Intraoperative imaging involves a computed tomography scan during surgery to evaluate surgical implants and restored anatomy and allows the clinician to correct errors in implant positioning that may occur during the same procedure. This article aims to demonstrate the potential clinical and cost saving benefits when both these technologies are used in orbital reconstruction which minimize the need for revision surgery.

Real-Time Digital Bright Field Technology for Rapid Antibiotic Susceptibility Testing.

Science.gov (United States)

Canali, Chiara; Spillum, Erik; Valvik, Martin; Agersnap, Niels; Olesen, Tom

2018-01-01

Optical scanning through bacterial samples and image-based analysis may provide a robust method for bacterial identification, fast estimation of growth rates and their modulation due to the presence of antimicrobial agents. Here, we describe an automated digital, time-lapse, bright field imaging system (oCelloScope, BioSense Solutions ApS, Farum, Denmark) for rapid and higher throughput antibiotic susceptibility testing (AST) of up to 96 bacteria-antibiotic combinations at a time. The imaging system consists of a digital camera, an illumination unit and a lens where the optical axis is tilted 6.25° relative to the horizontal plane of the stage. Such tilting grants more freedom of operation at both high and low concentrations of microorganisms. When considering a bacterial suspension in a microwell, the oCelloScope acquires a sequence of 6.25°-tilted images to form an image Z-stack. The stack contains the best-focus image, as well as the adjacent out-of-focus images (which contain progressively more out-of-focus bacteria, the further the distance from the best-focus position). The acquisition process is repeated over time, so that the time-lapse sequence of best-focus images is used to generate a video. The setting of the experiment, image analysis and generation of time-lapse videos can be performed through a dedicated software (UniExplorer, BioSense Solutions ApS). The acquired images can be processed for online and offline quantification of several morphological parameters, microbial growth, and inhibition over time.

Images from the Mind: BCI image reconstruction based on Rapid Serial Visual Presentations of polygon primitives

Directory of Open Access Journals (Sweden)

Luís F Seoane

2015-04-01

Full Text Available We provide a proof of concept for an EEG-based reconstruction of a visual image which is on a user's mind. Our approach is based on the Rapid Serial Visual Presentation (RSVP of polygon primitives and Brain-Computer Interface (BCI technology. In an experimental setup, subjects were presented bursts of polygons: some of them contributed to building a target image (because they matched the shape and/or color of the target while some of them did not. The presentation of the contributing polygons triggered attention-related EEG patterns. These Event Related Potentials (ERPs could be determined using BCI classification and could be matched to the stimuli that elicited them. These stimuli (i.e. the ERP-correlated polygons were accumulated in the display until a satisfactory reconstruction of the target image was reached. As more polygons were accumulated, finer visual details were attained resulting in more challenging classification tasks. In our experiments, we observe an average classification accuracy of around 75%. An in-depth investigation suggests that many of the misclassifications were not misinterpretations of the BCI concerning the users' intent, but rather caused by ambiguous polygons that could contribute to reconstruct several different images. When we put our BCI-image reconstruction in perspective with other RSVP BCI paradigms, there is large room for improvement both in speed and accuracy. These results invite us to be optimistic. They open a plethora of possibilities to explore non-invasive BCIs for image reconstruction both in healthy and impaired subjects and, accordingly, suggest interesting recreational and clinical applications.

Image Recommendation Algorithm Using Feature-Based Collaborative Filtering

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Kim, Deok-Hwan

As the multimedia contents market continues its rapid expansion, the amount of image contents used in mobile phone services, digital libraries, and catalog service is increasing remarkably. In spite of this rapid growth, users experience high levels of frustration when searching for the desired image. Even though new images are profitable to the service providers, traditional collaborative filtering methods cannot recommend them. To solve this problem, in this paper, we propose feature-based collaborative filtering (FBCF) method to reflect the user's most recent preference by representing his purchase sequence in the visual feature space. The proposed approach represents the images that have been purchased in the past as the feature clusters in the multi-dimensional feature space and then selects neighbors by using an inter-cluster distance function between their feature clusters. Various experiments using real image data demonstrate that the proposed approach provides a higher quality recommendation and better performance than do typical collaborative filtering and content-based filtering techniques.

Evaluation of chirp reversal power modulation sequence for contrast agent imaging

International Nuclear Information System (INIS)

Novell, A; Sennoga, CA; Escoffre, JM; Chaline, J; Bouakaz, A

2014-01-01

Over the last decade, significant research effort has been focused on the use of chirp for contrast agent imaging because chirps are known to significantly increase imaging contrast-to-noise ratio (CNR). New imaging schemes, such as chirp reversal (CR), have been developed to improve contrast detection by increasing non-linear microbubble responses. In this study we evaluated the contrast enhancement efficiency of various chirped imaging sequences in combination with well-established imaging schemes such as power modulation (PM) and pulse inversion (PI). The imaging schemes tested were implemented on a fully programmable open scanner and evaluated by ultrasonically scanning (excitation frequency of 2.5 MHz; amplitude of 350 kPa) a tissue-mimicking flow phantom comprising a 4 mm diameter tube through which aqueous dispersions (dilution fraction of 1/2000) of the commercial ultrasound contrast agent, SonoVue ® were continuously circulated. The recovery of non-linear microbubble responses after chirp compression requires the development and the optimization of a specific filter. A compression filter was therefore designed and used to compress and extract several non-linear components from the received microbubble responses. The results showed that using chirps increased the image CNR by approximately 10 dB, as compared to conventional Gaussian apodized sine burst excitation but degraded the axial resolution by a factor of 1.4, at −3 dB. We demonstrated that the highest CNR and contrast-to-noise ratio (CTR) were achievable when CR was combined with PM as compared to other imaging schemes such as PI. (paper)

Optimization of parameter values for complex pulse sequences by simulated annealing: application to 3D MP-RAGE imaging of the brain.

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Epstein, F H; Mugler, J P; Brookeman, J R

1994-02-01

A number of pulse sequence techniques, including magnetization-prepared gradient echo (MP-GRE), segmented GRE, and hybrid RARE, employ a relatively large number of variable pulse sequence parameters and acquire the image data during a transient signal evolution. These sequences have recently been proposed and/or used for clinical applications in the brain, spine, liver, and coronary arteries. Thus, the need for a method of deriving optimal pulse sequence parameter values for this class of sequences now exists. Due to the complexity of these sequences, conventional optimization approaches, such as applying differential calculus to signal difference equations, are inadequate. We have developed a general framework for adapting the simulated annealing algorithm to pulse sequence parameter value optimization, and applied this framework to the specific case of optimizing the white matter-gray matter signal difference for a T1-weighted variable flip angle 3D MP-RAGE sequence. Using our algorithm, the values of 35 sequence parameters, including the magnetization-preparation RF pulse flip angle and delay time, 32 flip angles in the variable flip angle gradient-echo acquisition sequence, and the magnetization recovery time, were derived. Optimized 3D MP-RAGE achieved up to a 130% increase in white matter-gray matter signal difference compared with optimized 3D RF-spoiled FLASH with the same total acquisition time. The simulated annealing approach was effective at deriving optimal parameter values for a specific 3D MP-RAGE imaging objective, and may be useful for other imaging objectives and sequences in this general class.

Scheduling algorithms for rapid imaging using agile Cubesat constellations

Science.gov (United States)

Nag, Sreeja; Li, Alan S.; Merrick, James H.

2018-02-01

Distributed Space Missions such as formation flight and constellations, are being recognized as important Earth Observation solutions to increase measurement samples over space and time. Cubesats are increasing in size (27U, ∼40 kg in development) with increasing capabilities to host imager payloads. Given the precise attitude control systems emerging in the commercial market, Cubesats now have the ability to slew and capture images within short notice. We propose a modular framework that combines orbital mechanics, attitude control and scheduling optimization to plan the time-varying, full-body orientation of agile Cubesats in a constellation such that they maximize the number of observed images and observation time, within the constraints of Cubesat hardware specifications. The attitude control strategy combines bang-bang and PD control, with constraints such as power consumption, response time, and stability factored into the optimality computations and a possible extension to PID control to account for disturbances. Schedule optimization is performed using dynamic programming with two levels of heuristics, verified and improved upon using mixed integer linear programming. The automated scheduler is expected to run on ground station resources and the resultant schedules uplinked to the satellites for execution, however it can be adapted for onboard scheduling, contingent on Cubesat hardware and software upgrades. The framework is generalizable over small steerable spacecraft, sensor specifications, imaging objectives and regions of interest, and is demonstrated using multiple 20 kg satellites in Low Earth Orbit for two case studies - rapid imaging of Landsat's land and coastal images and extended imaging of global, warm water coral reefs. The proposed algorithm captures up to 161% more Landsat images than nadir-pointing sensors with the same field of view, on a 2-satellite constellation over a 12-h simulation. Integer programming was able to verify that

Artifact free T2*-weighted imaging at high spatial resolution using segmented EPI sequences

International Nuclear Information System (INIS)

Heiler, Patrick Michael; Schad, Lothar Rudi; Schmitter, Sebastian

2010-01-01

The aim of this work was the development of novel measurement techniques that acquire high resolution T2 * -weighted datasets in measurement times as short as possible without suffering from noticeable blurring and ghosting artifacts. Therefore, two new measurement techniques were developed that acquire a smoother k-space than generic multi shot echo planar imaging sequences. One is based on the principle of echo train shifting, the other on the reversed gradient method. Simulations and phantom measurements demonstrate that echo train shifting works properly and reduces artifacts in multi shot echo planar imaging. For maximum SNR-efficiency this technique was further improved by adding a second contrast. Both contrasts can be acquired within a prolongation in measurement time by a factor of 1.5, leading to an SNR increase by approximately √2. Furthermore it is demonstrated that the reversed gradient method remarkably reduces artifacts caused by a discontinuous k-space weighting. Assuming sequence parameters as feasible for fMRI experiments, artifact free T2 * -weighted images with a matrix size of 256 x 256 leading to an in-plane resolution in the submillimeter range can be obtained in about 2 s per slice. (orig.)

Research on the Compression Algorithm of the Infrared Thermal Image Sequence Based on Differential Evolution and Double Exponential Decay Model

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Zhang, Jin-Yu; Meng, Xiang-Bing; Xu, Wei; Zhang, Wei; Zhang, Yong

2014-01-01

This paper has proposed a new thermal wave image sequence compression algorithm by combining double exponential decay fitting model and differential evolution algorithm. This study benchmarked fitting compression results and precision of the proposed method was benchmarked to that of the traditional methods via experiment; it investigated the fitting compression performance under the long time series and improved model and validated the algorithm by practical thermal image sequence compression and reconstruction. The results show that the proposed algorithm is a fast and highly precise infrared image data processing method. PMID:24696649

Research on the Compression Algorithm of the Infrared Thermal Image Sequence Based on Differential Evolution and Double Exponential Decay Model

Directory of Open Access Journals (Sweden)

Jin-Yu Zhang

2014-01-01

Full Text Available This paper has proposed a new thermal wave image sequence compression algorithm by combining double exponential decay fitting model and differential evolution algorithm. This study benchmarked fitting compression results and precision of the proposed method was benchmarked to that of the traditional methods via experiment; it investigated the fitting compression performance under the long time series and improved model and validated the algorithm by practical thermal image sequence compression and reconstruction. The results show that the proposed algorithm is a fast and highly precise infrared image data processing method.

First-pass myocardial perfusion MR imaging with gadolinium-enhanced turbo FLASH

International Nuclear Information System (INIS)

Teresi, L.M.; Smith, C.; Messenger, J.; Watanabe, A.; Herbst, M.; O'Sullivan, R.M.; Lee, R.; Remer, J.; Rappaport, A.; Bradley, W.G.

1990-01-01

This paper determines the efficacy of MR first-pass myocardial perfusion imaging using gadolinium-enhanced Turbo--fast low-angle shot (FLASH) ultrafast imaging combined with MR systolic wall thickening data for the determination of myocardial viability. Five normal volunteers and five patients with remote myocardial infarction were studied on a 1.5-T imaging system (Siemans, Ehrlangen, NJ). Turbo-FLASH imaging utilized a 180 degrees inversion pulse followed by a rapid gradient-echo sequence (TI 400 msec, TE2 msec, TR 4.9 msec, FA 8 degrees) with a complete 64 x 64 matrix image (300 mm FOV) being acquired in 300 msec. First-pass myocardial perfusion imaging was performed in the short-axis and long-axis oblique projections with a concantenated series of Turbo-FLASH images triggered to end-systole acquired immediately before and during a rapid bolus injection of 5cc gadolinium-DTPA

A rapid method for counting nucleated erythrocytes on stained blood smears by digital image analysis

Science.gov (United States)

Gering, E.; Atkinson, C.T.

2004-01-01

Measures of parasitemia by intraerythrocytic hematozoan parasites are normally expressed as the number of infected erythrocytes per n erythrocytes and are notoriously tedious and time consuming to measure. We describe a protocol for generating rapid counts of nucleated erythrocytes from digital micrographs of thin blood smears that can be used to estimate intensity of hematozoan infections in nonmammalian vertebrate hosts. This method takes advantage of the bold contrast and relatively uniform size and morphology of erythrocyte nuclei on Giemsa-stained blood smears and uses ImageJ, a java-based image analysis program developed at the U.S. National Institutes of Health and available on the internet, to recognize and count these nuclei. This technique makes feasible rapid and accurate counts of total erythrocytes in large numbers of microscope fields, which can be used in the calculation of peripheral parasitemias in low-intensity infections.

Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences.

Science.gov (United States)

Chen, Zhuo; Xu, Shixia; Zhou, Kaiya; Yang, Guang

2011-10-27

A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic relationships in the future.

Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences

Directory of Open Access Journals (Sweden)

Zhou Kaiya

2011-10-01

Full Text Available Abstract Background A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales, and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. Results An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae, and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Conclusions Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae, whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving

Rapid dual-tracer PTSM+ATSM PET imaging of tumour blood flow and hypoxia: a simulation study

International Nuclear Information System (INIS)

Rust, T C; Kadrmas, D J

2006-01-01

Blood flow and hypoxia are interrelated aspects of physiology that affect cancer treatment and response. Cu-PTSM and Cu-ATSM are related PET tracers for blood flow and hypoxia, and the ability to rapidly image both tracers in a single scan would bring several advantages over conventional single-tracer techniques. Using dynamic imaging with staggered injections, overlapping signals for multiple PET tracers may be recovered utilizing information from kinetics and radioactive decay. In this work, rapid dual-tracer PTSM+ATSM PET was simulated and tested as a function of injection delay, order and relative dose for several copper isotopes, and the results were compared relative to separate single-tracer data. Time-activity curves representing a broad range of tumour blood flow and hypoxia levels were simulated, and parallel dual-tracer compartment modelling was used to recover the signals for each tracer. The main results were tested further using a torso phantom simulation of PET tumour imaging. Using scans as short as 30 minutes, the dual-tracer method provided measures of blood flow and hypoxia similar to single-tracer imaging. The best performance was obtained by injecting PTSM first and using a somewhat higher dose for ATSM. Comparable results for different copper isotopes suggest that tracer kinetics with staggered injections play a more important role than radioactive decay in the signal separation process. Rapid PTSM+ATSM PET has excellent potential for characterizing both tumour blood flow and hypoxia in a single, fast scan, provided that technological hurdles related to algorithm development and routine use can be overcome

Fast imaging

International Nuclear Information System (INIS)

Wehrli, F.W.; Altas, S.W.

1991-01-01

This paper reports on MRI which has evolved rapidly and promises to continue to do so. The diagnostic armamentarium, as a result, has increased dramatically over recent years, which has necessitated constant interactions between clinicians, physicists, and biochemists. Pulse sequence design, coupled with advances in other software and hardware technology, offers practical improvements in scanning and image quality. Perhaps more importantly, these same advances hold promise for MRI to become, in addition to its traditional role as a morphological imaging technique, a functional imaging modality. The attractiveness of this prospect is that for the first time, a high-resolution technique has been shown to have the potential to provide both types of information from a single integrated examination, which promises to generate important insights into normal physiology as well as the natural history of pathophysiologic states

Basic evaluation of the new pulse sequence for simultaneous acquisition of T1- and T2-weighted images

International Nuclear Information System (INIS)

Kurose, Atsunari; Takahashi, Tohru; Ohishi, Tae; Ishikawa, Akihiro

2006-01-01

A novel pulse sequence that enables simultaneous acquisition of T1-weighted (T1W) and T2-weighted (T2W) images is presented. In this new technique, the inversion recovery (IR) pulse of conventional fast inversion recovery (Fast IR) is replaced with a pulse train that consists of a fast spin echo (FSE) and 180(y)+90(x) for driven inversion (DI). By using a shorter T1 and independent k-space ordering, the first part of the sequence provides T2W images and the second part provides T1W images, thereby enabling simultaneous acquisition in a single scan time comparable to that of Fast IR. Signal simulation also was conducted, and this was compared with conventional scanning techniques using normal volunteers. In the human studies, both T1W and T2W images showed the same image quality as conventional images, suggesting the potential for this technique to replace the combination of Fast IR and T2W FSE for scan-time reduction. (author)

INTEGRATED GEOREFERENCING OF STEREO IMAGE SEQUENCES CAPTURED WITH A STEREOVISION MOBILE MAPPING SYSTEM – APPROACHES AND PRACTICAL RESULTS

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H. Eugster

2012-07-01

Full Text Available Stereovision based mobile mapping systems enable the efficient capturing of directly georeferenced stereo pairs. With today's camera and onboard storage technologies imagery can be captured at high data rates resulting in dense stereo sequences. These georeferenced stereo sequences provide a highly detailed and accurate digital representation of the roadside environment which builds the foundation for a wide range of 3d mapping applications and image-based geo web-services. Georeferenced stereo images are ideally suited for the 3d mapping of street furniture and visible infrastructure objects, pavement inspection, asset management tasks or image based change detection. As in most mobile mapping systems, the georeferencing of the mapping sensors and observations – in our case of the imaging sensors – normally relies on direct georeferencing based on INS/GNSS navigation sensors. However, in urban canyons the achievable direct georeferencing accuracy of the dynamically captured stereo image sequences is often insufficient or at least degraded. Furthermore, many of the mentioned application scenarios require homogeneous georeferencing accuracy within a local reference frame over the entire mapping perimeter. To achieve these demands georeferencing approaches are presented and cost efficient workflows are discussed which allows validating and updating the INS/GNSS based trajectory with independently estimated positions in cases of prolonged GNSS signal outages in order to increase the georeferencing accuracy up to the project requirements.

Supervised detection of exoplanets in high-contrast imaging sequences

Science.gov (United States)

Gomez Gonzalez, C. A.; Absil, O.; Van Droogenbroeck, M.

2018-06-01

Context. Post-processing algorithms play a key role in pushing the detection limits of high-contrast imaging (HCI) instruments. State-of-the-art image processing approaches for HCI enable the production of science-ready images relying on unsupervised learning techniques, such as low-rank approximations, for generating a model point spread function (PSF) and subtracting the residual starlight and speckle noise. Aims: In order to maximize the detection rate of HCI instruments and survey campaigns, advanced algorithms with higher sensitivities to faint companions are needed, especially for the speckle-dominated innermost region of the images. Methods: We propose a reformulation of the exoplanet detection task (for ADI sequences) that builds on well-established machine learning techniques to take HCI post-processing from an unsupervised to a supervised learning context. In this new framework, we present algorithmic solutions using two different discriminative models: SODIRF (random forests) and SODINN (neural networks). We test these algorithms on real ADI datasets from VLT/NACO and VLT/SPHERE HCI instruments. We then assess their performances by injecting fake companions and using receiver operating characteristic analysis. This is done in comparison with state-of-the-art ADI algorithms, such as ADI principal component analysis (ADI-PCA). Results: This study shows the improved sensitivity versus specificity trade-off of the proposed supervised detection approach. At the diffraction limit, SODINN improves the true positive rate by a factor ranging from 2 to 10 (depending on the dataset and angular separation) with respect to ADI-PCA when working at the same false-positive level. Conclusions: The proposed supervised detection framework outperforms state-of-the-art techniques in the task of discriminating planet signal from speckles. In addition, it offers the possibility of re-processing existing HCI databases to maximize their scientific return and potentially improve

Functional MRI of the pharynx in obstructive sleep apnea (OSA) with rapid 2-D flash sequences

International Nuclear Information System (INIS)

Jaeger, L.; Guenther, E.; Gauger, J.; Nitz, W.; Kastenbauer, E.; Reiser, M.

1996-01-01

Functional imaging of the pharynx used to be the domain of cineradiography, CT and ultrafast CT. The development of modern MRI techniques led to new access to functional disorders of the pharynx. The aim of this study was to implement a new MRI technique to examine oropharyngeal obstructive mechanisms in patients with obstructive sleep apnea (OSA). Sixteen patients suffering from OSA and 6 healthy volunteers were examined on a 1.5 T whole-body imager ('Vision', Siemens, Erlangen Medical Engineering, Germany) using a circular polarized head coil. Imaging was performed with 2D flash sequences in midsagittal and axial planes. Patients and volunteers were asked to breathe normally through the nose and to simulate snoring and the Mueller maneuver during magnetic resonance imaging (MRI). Prior to MRI, all patients underwent an ear, nose and throat (ENT) examination, functional fiberoptic nasopharyngoscopy and polysomnography. A temporal resolution of 6 images/s and an in-plane resolution of 2.67x1.8 mm were achieved. The mobility of the tongue, soft palate and pharyngeal surface could be clearly delineated. The MRI findings correlated well with the clinical examinations. We propose ultrafast MRI as a reliable and non-invasive method of evaluating pharyngeal obstruction and their levels. (orig.) [de

Short echo time, fast gradient-echo imaging

International Nuclear Information System (INIS)

Haacke, E.M.; Lenz, G.W.

1987-01-01

Present fast-gradient-echoes schemes can acquire volume data rapidly and are flexible in T1 or T1/T2 contrast behavior. However, sequences used to date employ echo time (TE) values of about 15 ms +- 5 and, because of in vivo field inhomogeneities (short T2), they suffer badly from signal loss near sinuses and tissue boundaries. The authors implemented sequences with TE = 4-6 ms and found significant improvement in image quality, especially at high fields. Examples with long TEs vs. short TEs are given in the knee, spine, head, and orbits. Further advantages include (1) faster repetition times (15 ms), (2) higher-quality spin-density or T1-weighted images, and (3) reduction of blood motion artifacts

SWI or T2*: which MRI sequence to use in the detection of cerebral microbleeds? The Karolinska Imaging Dementia Study.

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Shams, S; Martola, J; Cavallin, L; Granberg, T; Shams, M; Aspelin, P; Wahlund, L O; Kristoffersen-Wiberg, M

2015-06-01

Cerebral microbleeds are thought to have potentially important clinical implications in dementia and stroke. However, the use of both T2* and SWI MR imaging sequences for microbleed detection has complicated the cross-comparison of study results. We aimed to determine the impact of microbleed sequences on microbleed detection and associated clinical parameters. Patients from our memory clinic (n = 246; 53% female; mean age, 62) prospectively underwent 3T MR imaging, with conventional thick-section T2*, thick-section SWI, and conventional thin-section SWI. Microbleeds were assessed separately on thick-section SWI, thin-section SWI, and T2* by 3 raters, with varying neuroradiologic experience. Clinical and radiologic parameters from the dementia investigation were analyzed in association with the number of microbleeds in negative binomial regression analyses. Prevalence and number of microbleeds were higher on thick-/thin-section SWI (20/21%) compared with T2*(17%). There was no difference in microbleed prevalence/number between thick- and thin-section SWI. Interrater agreement was excellent for all raters and sequences. Univariate comparisons of clinical parameters between patients with and without microbleeds yielded no difference across sequences. In the regression analysis, only minor differences in clinical associations with the number of microbleeds were noted across sequences. Due to the increased detection of microbleeds, we recommend SWI as the sequence of choice in microbleed detection. Microbleeds and their association with clinical parameters are robust to the effects of varying MR imaging sequences, suggesting that comparison of results across studies is possible, despite differing microbleed sequences. © 2015 by American Journal of Neuroradiology.

Subjective and objective image qualities: a comparison of sagittal T2 weighted spin-echo and turbo-spin-eco sequences in magnetic resonance imaging of the spine by use of a subjective ranking system

Energy Technology Data Exchange (ETDEWEB)

Goerres, G. [Institut fuer diagnostische Radiologie, Departement Radiologie, Universitaetskliniken, Kantonsspital Basel (Switzerland); Mader, I. [Radiologische Gemeinschaftspraxis Dres. Siems, Grossmann, Bayreuth (Germany); Proske, M. [Klinikum Rosenheim (Germany). Inst. fuer Diagnostische Radiologie

1998-12-31

We evaluated the subjective image impression of two different magnetic resonance (MR) sequences by using a subjective ranking system. This ranking system was based on 20 criteria describing several tissue characteristics such as the signal intensity of normal anatomical structures and the changes of signal intensities and shape of lesions as well as artefacts. MR of the vertebral spine was performed in 48 female and 52 male patients (mean age 44.8 years) referred consecutively for investigation of a back problem. Ninety-six pathologies were found in 82 patients. Sagittal and axial T1 weighted spin-echo before and after administration of Gadolinium (Gd-DOTA), and sagittal T2 weighted spin-echo (T2wSE) and Turbo-spin-echo (TSE) sequences were performed by means of surface coils. Using the subjective ranking system the sagittal T2wSE and sagittal TSE were compared. Both sequences were suitable for identification of normal anatomy and pathologic changes and there was no trend for increased detection of disease by one imaging sequence over the other. We found that sagittal TSE sequences can replace sagittal T2wSE sequences in spinal MR and that artefacts at the cervical and lumbar spine are less frequent using TSE, thus confirming previous studies. In this study, our ranking system reveiled, that there are differences between the subjective judgement of image qualities and objective measurement of SNR. However, this approach may not be helpful to compare two different MR sequences as it is limited to the anatomical area investigated and is time consuming. The subjective image impression, i.e. the quality of images, may not always be represented by physical parameters such as a signal-to-noise ratio (SNR), radiologists should try to define influences of image quality also by subjective parameters. (orig.)

PET Imaging Stability Measurements During Simultaneous Pulsing of Aggressive MR Sequences on the SIGNA PET/MR System.

Science.gov (United States)

Deller, Timothy W; Khalighi, Mohammad Mehdi; Jansen, Floris P; Glover, Gary H

2018-01-01

The recent introduction of simultaneous whole-body PET/MR scanners has enabled new research taking advantage of the complementary information obtainable with PET and MRI. One such application is kinetic modeling, which requires high levels of PET quantitative stability. To accomplish the required PET stability levels, the PET subsystem must be sufficiently isolated from the effects of MR activity. Performance measurements have previously been published, demonstrating sufficient PET stability in the presence of MR pulsing for typical clinical use; however, PET stability during radiofrequency (RF)-intensive and gradient-intensive sequences has not previously been evaluated for a clinical whole-body scanner. In this work, PET stability of the GE SIGNA PET/MR was examined during simultaneous scanning of aggressive MR pulse sequences. Methods: PET performance tests were acquired with MR idle and during simultaneous MR pulsing. Recent system improvements mitigating RF interference and gain variation were used. A fast recovery fast spin echo MR sequence was selected for high RF power, and an echo planar imaging sequence was selected for its high heat-inducing gradients. Measurements were performed to determine PET stability under varying MR conditions using the following metrics: sensitivity, scatter fraction, contrast recovery, uniformity, count rate performance, and image quantitation. A final PET quantitative stability assessment for simultaneous PET scanning during functional MRI studies was performed with a spiral in-and-out gradient echo sequence. Results: Quantitation stability of a 68 Ge flood phantom was demonstrated within 0.34%. Normalized sensitivity was stable during simultaneous scanning within 0.3%. Scatter fraction measured with a 68 Ge line source in the scatter phantom was stable within the range of 40.4%-40.6%. Contrast recovery and uniformity were comparable for PET images acquired simultaneously with multiple MR conditions. Peak noise equivalent count

A rapid and robust gradient measurement technique using dynamic single-point imaging.

Science.gov (United States)

Jang, Hyungseok; McMillan, Alan B

2017-09-01

We propose a new gradient measurement technique based on dynamic single-point imaging (SPI), which allows simple, rapid, and robust measurement of k-space trajectory. To enable gradient measurement, we utilize the variable field-of-view (FOV) property of dynamic SPI, which is dependent on gradient shape. First, one-dimensional (1D) dynamic SPI data are acquired from a targeted gradient axis, and then relative FOV scaling factors between 1D images or k-spaces at varying encoding times are found. These relative scaling factors are the relative k-space position that can be used for image reconstruction. The gradient measurement technique also can be used to estimate the gradient impulse response function for reproducible gradient estimation as a linear time invariant system. The proposed measurement technique was used to improve reconstructed image quality in 3D ultrashort echo, 2D spiral, and multi-echo bipolar gradient-echo imaging. In multi-echo bipolar gradient-echo imaging, measurement of the k-space trajectory allowed the use of a ramp-sampled trajectory for improved acquisition speed (approximately 30%) and more accurate quantitative fat and water separation in a phantom. The proposed dynamic SPI-based method allows fast k-space trajectory measurement with a simple implementation and no additional hardware for improved image quality. Magn Reson Med 78:950-962, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.

Science.gov (United States)

Vogel, Ulrich; Szczepanowski, Rafael; Claus, Heike; Jünemann, Sebastian; Prior, Karola; Harmsen, Dag

2012-06-01

Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers, and adolescents worldwide. DNA sequence-based typing, including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens, has become the standard for molecular epidemiology of the organism. However, PCR of multiple targets and consecutive Sanger sequencing provide logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next-generation sequencers (NGSs) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine (PGM) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus serogroup B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip-based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM technology generated sequence information for all target genes addressed. The results were 100% concordant with conventional typing results, with no further editing being necessary. In addition, the amount of typing information, i.e., nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In the near future, affordable and fast benchtop NGS machines like the PGM might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workloads and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability, and antibiotic resistance gene monitoring.

Particle tracking from image sequences of complex plasma crystals

International Nuclear Information System (INIS)

Hadziavdic, Vedad; Melandsoe, Frank; Hanssen, Alfred

2006-01-01

In order to gather information about the physics of the complex plasma crystals from the experimental data, particles have to be tracked through a sequence of images. An application of the Kalman filter for that purpose is presented, using a one-dimensional approximation of the particle dynamics as a model for the filter. It is shown that Kalman filter is capable of tracking dust particles even with high levels of measurement noise. An inherent part of the Kalman filter, the innovation process, can be used to estimate values of the physical system parameters from the experimental data. The method is shown to be able to estimate the characteristic oscillation frequency from noisy data

Thickness of patellofemoral articular cartilage as measured on MR imaging: sequence comparison of accuracy, reproducibility, and interobserver variation

Energy Technology Data Exchange (ETDEWEB)

Van Leersum, M.D. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Schweitzer, M.E. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Gannon, F. [Dept. of Pathology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Vinitski, S. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Finkel, G. [Dept. of Pathology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Mitchell, D.G. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States)

1995-08-01

This study was undertaken to assess the accuracy, precision, and reliability of magnetic resonance (MR) measurements of articular cartilage. Fifteen cadaveric patellas were imaged in the axial plane at 1.5 T. Gradient echo and fat-suppressed FSE, T2-weighted, proton density, and T1-weighted sequences were performed. We measured each 5-mm section separately at three standardized positions, giving a total of 900 measurements. These findings were correlated with independently performed measurements of the corresponding anatomic sections. A hundred random measurements were also evaluated for reproducibility and interobserver variation. Although all sequences were highly accurate, the T1-weighted images were the most accurate, with a mean difference of 0.25 mm and a correlation coefficient of 0.85. All sequences were also highly reproducible with little inter-observer variation. In an attempt to improve the accuracy of the MR measurements further, we retrospectively evaluated all measurements with discrepancies greater than 1 mm from the specimen. All these differences were attributable to focal defects causing exaggeration of the thickness on MR imaging. (orig.)

Thickness of patellofemoral articular cartilage as measured on MR imaging: sequence comparison of accuracy, reproducibility, and interobserver variation

International Nuclear Information System (INIS)

Van Leersum, M.D.; Schweitzer, M.E.; Gannon, F.; Vinitski, S.; Finkel, G.; Mitchell, D.G.

1995-01-01

This study was undertaken to assess the accuracy, precision, and reliability of magnetic resonance (MR) measurements of articular cartilage. Fifteen cadaveric patellas were imaged in the axial plane at 1.5 T. Gradient echo and fat-suppressed FSE, T2-weighted, proton density, and T1-weighted sequences were performed. We measured each 5-mm section separately at three standardized positions, giving a total of 900 measurements. These findings were correlated with independently performed measurements of the corresponding anatomic sections. A hundred random measurements were also evaluated for reproducibility and interobserver variation. Although all sequences were highly accurate, the T1-weighted images were the most accurate, with a mean difference of 0.25 mm and a correlation coefficient of 0.85. All sequences were also highly reproducible with little inter-observer variation. In an attempt to improve the accuracy of the MR measurements further, we retrospectively evaluated all measurements with discrepancies greater than 1 mm from the specimen. All these differences were attributable to focal defects causing exaggeration of the thickness on MR imaging. (orig.)

Fast triple-spin-echo Dixon (FTSED) sequence for water and fat imaging

Czech Academy of Sciences Publication Activity Database

Kořínek, Radim; Bartušek, Karel; Starčuk jr., Zenon

2017-01-01

Roč. 37, APR (2017), s. 164-170 ISSN 0730-725X R&D Projects: GA MŠk ED0017/01/01; GA MŠk(CZ) LO1212 Institutional support: RVO:68081731 Keywords : fast triple-spin-echo Dixon * sequence * MRI * fat fraction * water-fat * ultra-high field * 9.4 T * FTSED Subject RIV: BH - Optics, Masers, Lasers OBOR OECD: Radiology, nuclear medicine and medical imaging Impact factor: 2.225, year: 2016

Alu polymerase chain reaction: A method for rapid isolation of human-specific sequences from complex DNA sources

International Nuclear Information System (INIS)

Nelson, D.L.; Ledbetter, S.A.; Corbo, L.; Victoria, M.F.; Ramirez-Solis, R.; Webster, T.D.; Ledbetter, D.H.; Caskey, C.T.

1989-01-01

Current efforts to map the human genome are focused on individual chromosomes or smaller regions and frequently rely on the use of somatic cell hybrids. The authors report the application of the polymerase chain reaction to direct amplification of human DNA from hybrid cells containing regions of the human genome in rodent cell backgrounds using primers directed to the human Alu repeat element. They demonstrate Alu-directed amplification of a fragment of the human HPRT gene from both hybrid cell and cloned DNA and identify through sequence analysis the Alu repeats involved in this amplification. They also demonstrate the application of this technique to identify the chromosomal locations of large fragments of the human X chromosome cloned in a yeast artificial chromosome and the general applicability of the method to the preparation of DNA probes from cloned human sequences. The technique allows rapid gene mapping and provides a simple method for the isolation and analysis of specific chromosomal regions

A probabilistic cell model in background corrected image sequences for single cell analysis

Directory of Open Access Journals (Sweden)

Fieguth Paul

2010-10-01

Full Text Available Abstract Background Methods of manual cell localization and outlining are so onerous that automated tracking methods would seem mandatory for handling huge image sequences, nevertheless manual tracking is, astonishingly, still widely practiced in areas such as cell biology which are outside the influence of most image processing research. The goal of our research is to address this gap by developing automated methods of cell tracking, localization, and segmentation. Since even an optimal frame-to-frame association method cannot compensate and recover from poor detection, it is clear that the quality of cell tracking depends on the quality of cell detection within each frame. Methods Cell detection performs poorly where the background is not uniform and includes temporal illumination variations, spatial non-uniformities, and stationary objects such as well boundaries (which confine the cells under study. To improve cell detection, the signal to noise ratio of the input image can be increased via accurate background estimation. In this paper we investigate background estimation, for the purpose of cell detection. We propose a cell model and a method for background estimation, driven by the proposed cell model, such that well structure can be identified, and explicitly rejected, when estimating the background. Results The resulting background-removed images have fewer artifacts and allow cells to be localized and detected more reliably. The experimental results generated by applying the proposed method to different Hematopoietic Stem Cell (HSC image sequences are quite promising. Conclusion The understanding of cell behavior relies on precise information about the temporal dynamics and spatial distribution of cells. Such information may play a key role in disease research and regenerative medicine, so automated methods for observation and measurement of cells from microscopic images are in high demand. The proposed method in this paper is capable

Time integration and statistical regulation applied to mobile objects detection in a sequence of images

International Nuclear Information System (INIS)

Letang, Jean-Michel

1993-01-01

This PhD thesis deals with the detection of moving objects in monocular image sequences. The first section presents the inherent problems of motion analysis in real applications. We propose a method robust to perturbations frequently encountered during acquisition of outdoor scenes. It appears three main directions for investigations, all of them pointing out the importance of the temporal axis, which is a specific dimension for motion analysis. In the first part, the image sequence is considered as a set of temporal signals. The temporal multi-scale decomposition enables the characterization of various dynamical behaviors of the objects being in the scene at a given instant. A second module integrates motion information. This elementary trajectography of moving objects provides a temporal prediction map, giving a confidence level of motion presence. Interactions between both sets of data are expressed within a statistical regularization. Markov random field models supply a formal framework to convey a priori knowledge of the primitives to be evaluated. A calibration method with qualitative boxes is presented to estimate model parameters. Our approach requires only simple computations and leads to a rather fast algorithm, that we evaluate in the last section over various typical sequences. (author) [fr

Automated Detection of Buildings from Heterogeneous VHR Satellite Images for Rapid Response to Natural Disasters

Directory of Open Access Journals (Sweden)

Shaodan Li

2017-11-01

Full Text Available In this paper, we present a novel approach for automatically detecting buildings from multiple heterogeneous and uncalibrated very high-resolution (VHR satellite images for a rapid response to natural disasters. In the proposed method, a simple and efficient visual attention method is first used to extract built-up area candidates (BACs from each multispectral (MS satellite image. After this, morphological building indices (MBIs are extracted from all the masked panchromatic (PAN and MS images with BACs to characterize the structural features of buildings. Finally, buildings are automatically detected in a hierarchical probabilistic model by fusing the MBI and masked PAN images. The experimental results show that the proposed method is comparable to supervised classification methods in terms of recall, precision and F-value.

Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD): exome sequencing of trios, monozygotic twins and tumours

OpenAIRE

Barclay, Sarah F.; Rand, Casey M.; Borch, Lauren A.; Nguyen, Lisa; Gray, Paul A.; Gibson, William T.; Wilson, Richard J. A.; Gordon, Paul M. K.; Aung, Zaw; Berry-Kravis, Elizabeth M.; Ize-Ludlow, Diego; Weese-Mayer, Debra E.; Bech-Hansen, N. Torben

2015-01-01

Background Rapid-onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD) is thought to be a genetic disease caused by de novo mutations, though causative mutations have yet to be identified. We searched for de novo coding mutations among a carefully-diagnosed and clinically homogeneous cohort of 35 ROHHAD patients. Methods We sequenced the exomes of seven ROHHAD trios, plus tumours from four of these patients and the unaffected monozygotic (MZ) twin ...

Automated Leaf Tracking using Multi-view Image Sequences of Maize Plants for Leaf-growth Monitoring

Science.gov (United States)

Das Choudhury, S.; Awada, T.; Samal, A.; Stoerger, V.; Bashyam, S.

2017-12-01

Extraction of phenotypes with botanical importance by analyzing plant image sequences has the desirable advantages of non-destructive temporal phenotypic measurements of a large number of plants with little or no manual intervention in a relatively short period of time. The health of a plant is best interpreted by the emergence timing and temporal growth of individual leaves. For automated leaf growth monitoring, it is essential to track each leaf throughout the life cycle of the plant. Plants are constantly changing organisms with increasing complexity in architecture due to variations in self-occlusions and phyllotaxy, i.e., arrangements of leaves around the stem. The leaf cross-overs pose challenges to accurately track each leaf using single view image sequence. Thus, we introduce a novel automated leaf tracking algorithm using a graph theoretic approach by multi-view image sequence analysis based on the determination of leaf-tips and leaf-junctions in the 3D space. The basis of the leaf tracking algorithm is: the leaves emerge using bottom-up approach in the case of a maize plant, and the direction of leaf emergence strictly alternates in terms of direction. The algorithm involves labeling of the individual parts of a plant, i.e., leaves and stem, following graphical representation of the plant skeleton, i.e., one-pixel wide connected line obtained from the binary image. The length of the leaf is measured by the number of pixels in the leaf skeleton. To evaluate the performance of the algorithm, a benchmark dataset is indispensable. Thus, we publicly release University of Nebraska-Lincoln Component Plant Phenotyping dataset-2 (UNL-CPPD-2) consisting of images of the 20 maize plants captured by visible light camera of the Lemnatec Scanalyzer 3D high throughout plant phenotyping facility once daily for 60 days from 10 different views. The dataset is aimed to facilitate the development and evaluation of leaf tracking algorithms and their uniform comparisons.

Easy Leaf Area: Automated digital image analysis for rapid and accurate measurement of leaf area.

Science.gov (United States)

Easlon, Hsien Ming; Bloom, Arnold J

2014-07-01

Measurement of leaf areas from digital photographs has traditionally required significant user input unless backgrounds are carefully masked. Easy Leaf Area was developed to batch process hundreds of Arabidopsis rosette images in minutes, removing background artifacts and saving results to a spreadsheet-ready CSV file. • Easy Leaf Area uses the color ratios of each pixel to distinguish leaves and calibration areas from their background and compares leaf pixel counts to a red calibration area to eliminate the need for camera distance calculations or manual ruler scale measurement that other software methods typically require. Leaf areas estimated by this software from images taken with a camera phone were more accurate than ImageJ estimates from flatbed scanner images. • Easy Leaf Area provides an easy-to-use method for rapid measurement of leaf area and nondestructive estimation of canopy area from digital images.

Rapid Development of Microsatellite Markers for Plantago ovata Forsk.: Using Next Generation Sequencing and Their Cross-Species Transferability

Directory of Open Access Journals (Sweden)

Ranbir Singh Fougat

2014-06-01

Full Text Available Isabgol (Plantago ovata Forsk. is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™ to obtain simple sequence repeats (SSRs for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata.

Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building.

Science.gov (United States)

Pomerantz, Aaron; Peñafiel, Nicolás; Arteaga, Alejandro; Bustamante, Lucas; Pichardo, Frank; Coloma, Luis A; Barrio-Amorós, César L; Salazar-Valenzuela, David; Prost, Stefan

2018-04-01

Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here, we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack in one of the world's most imperiled biodiversity hotspots, the Ecuadorian Chocó rainforest. We used portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, polymerase chain reaction amplification, and real-time DNA barcoding of reptile specimens in the field. We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. The flexibility of our mobile laboratory further allowed us to generate sequence information at the Universidad Tecnológica Indoamérica in Quito for rare, endangered, and undescribed species. This includes the recently rediscovered Jambato toad, which was thought to be extinct for 28 years. Sequences generated on the MinION required as few as 30 reads to achieve high accuracy relative to Sanger sequencing, and with further multiplexing of samples, nanopore sequencing can become a cost-effective approach for rapid and portable DNA barcoding. Overall, we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas to aid in conservation efforts and be applied to research facilities in developing countries. This opens up possibilities for biodiversity studies by promoting local research capacity building, teaching nonspecialists and students about the environment, tackling wildlife crime, and promoting conservation via research-focused ecotourism.

Whole-body magnetic resonance imaging for staging and follow-up of pediatric patients with Hodgkin's lymphoma: comparison of different sequences

International Nuclear Information System (INIS)

Nava, Daniel; Oliveira, Heverton Cesar de

2011-01-01

Objective: to compare the performance of the T1, T2, STIR and DWIBS (diffusion-weighted whole-body imaging with background body signal suppression) sequences in the staging and follow-up of pediatric patients with Hodgkin's lymphoma in lymph node chains, parenchymal organs and bone marrow, and to evaluate interobserver agreement. Materials and methods: the authors studied 12 patients with confirmed diagnosis of Hodgkin's lymphoma. The patients were referred for whole body magnetic resonance imaging with T1-weighted, T2-weighted, STIR and DWIBS sequences. Results: the number of lymph node sites characterized as affected by the disease on T1- and T2-weighted sequences showed similar results (8 sites for both sequences), but lower than DWIBS and STIR sequences (11 and 12 sites, respectively). The bone marrow involvement by lymphoma showed the same values for the T1-, T2-weighted and DWIBS sequences (17 lesions), higher than the value found on STIR (13 lesions). A high rate of interobserver agreement was observed as the four sequences were analyzed. Conclusion: STIR and DWIBS sequences detected the highest number of lymph node sites characterized as affected by the disease. Similar results were demonstrated by all the sequences in the evaluation of parenchymal organs and bone marrow. A high interobserver agreement was observed as the four sequences were analyzed. (author)

Contrast-enhanced Magnetic Resonance Imaging of Pelvic Bone Metastases at 3.0 T: Comparison Between 3-dimensional T1-weighted CAIPIRINHA-VIBE Sequence and 2-dimensional T1-weighted Turbo Spin-Echo Sequence.

Science.gov (United States)

Yoon, Min A; Hong, Suk-Joo; Lee, Kyu-Chong; Lee, Chang Hee

2018-06-12

This study aimed to compare 3-dimensional T1-weighted gradient-echo sequence (CAIPIRINHA-volumetric interpolated breath-hold examination [VIBE]) with 2-dimensional T1-weighted turbo spin-echo sequence for contrast-enhanced magnetic resonance imaging (MRI) of pelvic bone metastases at 3.0 T. Thirty-one contrast-enhanced MRIs of pelvic bone metastases were included. Two contrast-enhanced sequences were evaluated for the following parameters: overall image quality, sharpness of pelvic bone, iliac vessel clarity, artifact severity, and conspicuity and edge sharpness of the smallest metastases. Quantitative analysis was performed by calculating signal-to-noise ratio and contrast-to-noise ratio of the smallest metastases. Significant differences between the 2 sequences were assessed. CAIPIRINHA-VIBE had higher scores for overall image quality, pelvic bone sharpness, iliac vessel clarity, and edge sharpness of the metastatic lesions, and had less artifacts (all P 0.05). Our results suggest that CAIPIRINHA-VIBE may be superior to turbo spin-echo for contrast-enhanced MRI of pelvic bone metastases at 3.0 T.

Digital Sequences and a Time Reversal-Based Impact Region Imaging and Localization Method

Science.gov (United States)

Qiu, Lei; Yuan, Shenfang; Mei, Hanfei; Qian, Weifeng

2013-01-01

To reduce time and cost of damage inspection, on-line impact monitoring of aircraft composite structures is needed. A digital monitor based on an array of piezoelectric transducers (PZTs) is developed to record the impact region of impacts on-line. It is small in size, lightweight and has low power consumption, but there are two problems with the impact alarm region localization method of the digital monitor at the current stage. The first one is that the accuracy rate of the impact alarm region localization is low, especially on complex composite structures. The second problem is that the area of impact alarm region is large when a large scale structure is monitored and the number of PZTs is limited which increases the time and cost of damage inspections. To solve the two problems, an impact alarm region imaging and localization method based on digital sequences and time reversal is proposed. In this method, the frequency band of impact response signals is estimated based on the digital sequences first. Then, characteristic signals of impact response signals are constructed by sinusoidal modulation signals. Finally, the phase synthesis time reversal impact imaging method is adopted to obtain the impact region image. Depending on the image, an error ellipse is generated to give out the final impact alarm region. A validation experiment is implemented on a complex composite wing box of a real aircraft. The validation results show that the accuracy rate of impact alarm region localization is approximately 100%. The area of impact alarm region can be reduced and the number of PZTs needed to cover the same impact monitoring region is reduced by more than a half. PMID:24084123

Capillary gel electrophoresis for rapid, high resolution DNA sequencing.

OpenAIRE

Swerdlow, H; Gesteland, R

1990-01-01

Capillary gel electrophoresis has been demonstrated for the separation and detection of DNA sequencing samples. Enzymatic dideoxy nucleotide chain termination was employed, using fluorescently tagged oligonucleotide primers and laser based on-column detection (limit of detection is 6,000 molecules per peak). Capillary gel separations were shown to be three times faster, with better resolution (2.4 x), and higher separation efficiency (5.4 x) than a conventional automated slab gel DNA sequenci...

Three-dimensional true FISP for high-resolution imaging of the whole brain

International Nuclear Information System (INIS)

Schmitz, B.; Hagen, T.; Reith, W.

2003-01-01

While high-resolution T1-weighted sequences, such as three-dimensional magnetization-prepared rapid gradient-echo imaging, are widely available, there is a lack of an equivalent fast high-resolution sequence providing T2 contrast. Using fast high-performance gradient systems we show the feasibility of three-dimensional true fast imaging with steady-state precession (FISP) to fill this gap. We applied a three-dimensional true-FISP protocol with voxel sizes down to 0.5 x 0.5 x 0.5 mm and acquisition times of approximately 8 min on a 1.5-T Sonata (Siemens, Erlangen, Germany) magnetic resonance scanner. The sequence was included into routine brain imaging protocols for patients with cerebrospinal-fluid-related intracranial pathology. Images from 20 patients and 20 healthy volunteers were evaluated by two neuroradiologists with respect to diagnostic image quality and artifacts. All true-FISP scans showed excellent imaging quality free of artifacts in patients and volunteers. They were valuable for the assessment of anatomical and pathologic aspects of the included patients. High-resolution true-FISP imaging is a valuable adjunct for the exploration and neuronavigation of intracranial pathologies especially if cerebrospinal fluid is involved. (orig.)

MR Fingerprinting for Rapid Quantitative Abdominal Imaging.

Science.gov (United States)

Chen, Yong; Jiang, Yun; Pahwa, Shivani; Ma, Dan; Lu, Lan; Twieg, Michael D; Wright, Katherine L; Seiberlich, Nicole; Griswold, Mark A; Gulani, Vikas

2016-04-01

To develop a magnetic resonance (MR) "fingerprinting" technique for quantitative abdominal imaging. This HIPAA-compliant study had institutional review board approval, and informed consent was obtained from all subjects. To achieve accurate quantification in the presence of marked B0 and B1 field inhomogeneities, the MR fingerprinting framework was extended by using a two-dimensional fast imaging with steady-state free precession, or FISP, acquisition and a Bloch-Siegert B1 mapping method. The accuracy of the proposed technique was validated by using agarose phantoms. Quantitative measurements were performed in eight asymptomatic subjects and in six patients with 20 focal liver lesions. A two-tailed Student t test was used to compare the T1 and T2 results in metastatic adenocarcinoma with those in surrounding liver parenchyma and healthy subjects. Phantom experiments showed good agreement with standard methods in T1 and T2 after B1 correction. In vivo studies demonstrated that quantitative T1, T2, and B1 maps can be acquired within a breath hold of approximately 19 seconds. T1 and T2 measurements were compatible with those in the literature. Representative values included the following: liver, 745 msec ± 65 (standard deviation) and 31 msec ± 6; renal medulla, 1702 msec ± 205 and 60 msec ± 21; renal cortex, 1314 msec ± 77 and 47 msec ± 10; spleen, 1232 msec ± 92 and 60 msec ± 19; skeletal muscle, 1100 msec ± 59 and 44 msec ± 9; and fat, 253 msec ± 42 and 77 msec ± 16, respectively. T1 and T2 in metastatic adenocarcinoma were 1673 msec ± 331 and 43 msec ± 13, respectively, significantly different from surrounding liver parenchyma relaxation times of 840 msec ± 113 and 28 msec ± 3 (P < .0001 and P < .01) and those in hepatic parenchyma in healthy volunteers (745 msec ± 65 and 31 msec ± 6, P < .0001 and P = .021, respectively). A rapid technique for quantitative abdominal imaging was developed that allows simultaneous quantification of multiple tissue

Analysis of Gradient Waveform in Magnetic Resonance Imaging

Directory of Open Access Journals (Sweden)

OU-YANG Shan-mei

2017-12-01

Full Text Available The accuracy of gradient pulse waveform affects image quality significantly in magnetic resonance imaging (MRI. Recording and analyzing the waveform of gradient pulse helps to make rapid and accurate diagnosis of spectrometer gradient hardware and/or pulse sequence. Using the virtual instrument software LabVIEW to control the high speed data acquisition card DAQ-2005, a multi-channel acquisition scheme was designed to collect the gradient outputs from a custom-made spectrometer. The collected waveforms were post-processed (i.e., histogram statistical analysis, data filtering and difference calculation to obtain feature points containing time and amplitude information. Experiments were carried out to validate the method, which is an auxiliary test method for the development of spectrometer and pulses sequence.

Correction of projective distortion in long-image-sequence mosaics without prior information

Science.gov (United States)

Yang, Chenhui; Mao, Hongwei; Abousleman, Glen; Si, Jennie

2010-04-01

Image mosaicking is the process of piecing together multiple video frames or still images from a moving camera to form a wide-area or panoramic view of the scene being imaged. Mosaics have widespread applications in many areas such as security surveillance, remote sensing, geographical exploration, agricultural field surveillance, virtual reality, digital video, and medical image analysis, among others. When mosaicking a large number of still images or video frames, the quality of the resulting mosaic is compromised by projective distortion. That is, during the mosaicking process, the image frames that are transformed and pasted to the mosaic become significantly scaled down and appear out of proportion with respect to the mosaic. As more frames continue to be transformed, important target information in the frames can be lost since the transformed frames become too small, which eventually leads to the inability to continue further. Some projective distortion correction techniques make use of prior information such as GPS information embedded within the image, or camera internal and external parameters. Alternatively, this paper proposes a new algorithm to reduce the projective distortion without using any prior information whatsoever. Based on the analysis of the projective distortion, we approximate the projective matrix that describes the transformation between image frames using an affine model. Using singular value decomposition, we can deduce the affine model scaling factor that is usually very close to 1. By resetting the image scale of the affine model to 1, the transformed image size remains unchanged. Even though the proposed correction introduces some error in the image matching, this error is typically acceptable and more importantly, the final mosaic preserves the original image size after transformation. We demonstrate the effectiveness of this new correction algorithm on two real-world unmanned air vehicle (UAV) sequences. The proposed method is

The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software

Science.gov (United States)

Lucas, Blake C.; Bogovic, John A.; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L.; Pham, Dzung

2010-01-01

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). PMID:20077162

The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software.

Science.gov (United States)

Lucas, Blake C; Bogovic, John A; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L; Pham, Dzung L; Landman, Bennett A

2010-03-01

Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).

[Study on method of tracking the active cells in image sequences based on EKF-PF].

Science.gov (United States)

Tang, Chunming; Liu, Ying

2013-02-01

In cell image sequences, due to the nonlinear and nonGaussian motion characteristics of active cells, the accurate prediction and tracking is still an unsolved problem. We applied extended Kalman particle filter (EKF-PF) here in our study, attempting to solve the problem. Firstly we confirmed the existence and positions of the active cells. Then we established a motion model and improved it via adding motion angle estimation. Next we predicted motion parameters, such as displacement, velocity, accelerated velocity and motion angle, in region centers of the cells being tracked. Finally we obtained the motion traces of active cells. There were fourteen active cells in three image sequences which have been tracked. The errors were less than 2.5 pixels when the prediction values were compared with actual values. It showed that the presented algorithm may basically reach the solution of accurate predition and tracking of the active cells.

Artifact free T2{sup *}-weighted imaging at high spatial resolution using segmented EPI sequences

Energy Technology Data Exchange (ETDEWEB)

Heiler, Patrick Michael; Schad, Lothar Rudi [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Schmitter, Sebastian [German Cancer Research Center, Heidelberg (Germany). Dept. of Medical Physics in Radiology

2010-07-01

The aim of this work was the development of novel measurement techniques that acquire high resolution T2{sup *}-weighted datasets in measurement times as short as possible without suffering from noticeable blurring and ghosting artifacts. Therefore, two new measurement techniques were developed that acquire a smoother k-space than generic multi shot echo planar imaging sequences. One is based on the principle of echo train shifting, the other on the reversed gradient method. Simulations and phantom measurements demonstrate that echo train shifting works properly and reduces artifacts in multi shot echo planar imaging. For maximum SNR-efficiency this technique was further improved by adding a second contrast. Both contrasts can be acquired within a prolongation in measurement time by a factor of 1.5, leading to an SNR increase by approximately {radical}2. Furthermore it is demonstrated that the reversed gradient method remarkably reduces artifacts caused by a discontinuous k-space weighting. Assuming sequence parameters as feasible for fMRI experiments, artifact free T2{sup *}-weighted images with a matrix size of 256 x 256 leading to an in-plane resolution in the submillimeter range can be obtained in about 2 s per slice. (orig.)

Diagnostic value of the fast-FLAIR sequence in MR imaging of intracranial tumors

International Nuclear Information System (INIS)

Husstedt, H.W.; Sickert, M.; Koestler, H.; Haubitz, B.; Becker, H.

2000-01-01

The aim of this study was to quantify imaging characteristics of fast fluid-attenuated inversion recovery (FLAIR) sequence in brain tumors compared with T1-postcontrast- and T2-sequences. Fast-FLAIR-, T2 fast spin echo (FSE)-, and T1 SE postcontrast images of 74 patients with intracranial neoplasms were analyzed. Four neuroradiologists rated signal intensity and inhomogeneity of the tumor, rendering of cystic parts, demarcation of the tumor vs brain, of the tumor vs edema and of brain vs edema, as well as the presence of motion and of other artifacts. Data analysis was performed for histologically proven astrocytomas, glioblastomas, and meningiomas, for tumors with poor contrast enhancement, and for all patients pooled. Only for tumors with poor contrast enhancement (n = 12) did fast FLAIR provide additional information about the lesion. In these cases, signal intensity, demarcation of the tumor vs brain, and differentiation of the tumor vs edema were best using fast FLAIR. In all cases, rendering of the tumor's inner structure was poor. For all other tumor types, fast FLAIR did not give clinically relevant information, the only exception being a better demarcation of the edema from brain tissue. Artifacts rarely interfered with evaluation of fast-FLAIR images. Thus, fast FLAIR cannot replace T2-weighted series. It provides additional information only in tumors with poor contrast enhancement. It is helpful for defining the exact extent of the edema of any tumor but gives little information about their inner structure. (orig.)

Diagnostic value of the fast-FLAIR sequence in MR imaging of intracranial tumors.

Science.gov (United States)

Husstedt, H W; Sickert, M; Köstler, H; Haubitz, B; Becker, H

2000-01-01

The aim of this study was to quantify imaging characteristics of fast fluid-attenuated inversion recovery (FLAIR) sequence in brain tumors compared with T1-postcontrast- and T2-sequences. Fast-FLAIR-, T2 fast spin echo (FSE)-, and T1 SE postcontrast images of 74 patients with intracranial neoplasms were analyzed. Four neuroradiologists rated signal intensity and inhomogeneity of the tumor, rendering of cystic parts, demarcation of the tumor vs brain, of the tumor vs edema and of brain vs edema, as well as the presence of motion and of other artifacts. Data analysis was performed for histologically proven astrocytomas, glioblastomas, and meningiomas, for tumors with poor contrast enhancement, and for all patients pooled. Only for tumors with poor contrast enhancement (n = 12) did fast FLAIR provide additional information about the lesion. In these cases, signal intensity, demarcation of the tumor vs brain, and differentiation of the tumor vs edema were best using fast FLAIR. In all cases, rendering of the tumor's inner structure was poor. For all other tumor types, fast FLAIR did not give clinically relevant information, the only exception being a better demarcation of the edema from brain tissue. Artifacts rarely interfered with evaluation of fast-FLAIR images. Thus, fast FLAIR cannot replace T2-weighted series. It provides additional information only in tumors with poor contrast enhancement. It is helpful for defining the exact extent of the edema of any tumor but gives little information about their inner structure.

A Low-Cost PC-Based Image Workstation for Dynamic Interactive Display of Three-Dimensional Anatomy

Science.gov (United States)

Barrett, William A.; Raya, Sai P.; Udupa, Jayaram K.

1989-05-01

A system for interactive definition, automated extraction, and dynamic interactive display of three-dimensional anatomy has been developed and implemented on a low-cost PC-based image workstation. An iconic display is used for staging predefined image sequences through specified increments of tilt and rotation over a solid viewing angle. Use of a fast processor facilitates rapid extraction and rendering of the anatomy into predefined image views. These views are formatted into a display matrix in a large image memory for rapid interactive selection and display of arbitrary spatially adjacent images within the viewing angle, thereby providing motion parallax depth cueing for efficient and accurate perception of true three-dimensional shape, size, structure, and spatial interrelationships of the imaged anatomy. The visual effect is that of holding and rotating the anatomy in the hand.

Rapid wide-field Mueller matrix polarimetry imaging based on four photoelastic modulators with no moving parts.

Science.gov (United States)

Alali, Sanaz; Gribble, Adam; Vitkin, I Alex

2016-03-01

A new polarimetry method is demonstrated to image the entire Mueller matrix of a turbid sample using four photoelastic modulators (PEMs) and a charge coupled device (CCD) camera, with no moving parts. Accurate wide-field imaging is enabled with a field-programmable gate array (FPGA) optical gating technique and an evolutionary algorithm (EA) that optimizes imaging times. This technique accurately and rapidly measured the Mueller matrices of air, polarization elements, and turbid phantoms. The system should prove advantageous for Mueller matrix analysis of turbid samples (e.g., biological tissues) over large fields of view, in less than a second.

A spiral-based volumetric acquisition for MR temperature imaging.

Science.gov (United States)

Fielden, Samuel W; Feng, Xue; Zhao, Li; Miller, G Wilson; Geeslin, Matthew; Dallapiazza, Robert F; Elias, W Jeffrey; Wintermark, Max; Butts Pauly, Kim; Meyer, Craig H

2018-06-01

To develop a rapid pulse sequence for volumetric MR thermometry. Simulations were carried out to assess temperature deviation, focal spot distortion/blurring, and focal spot shift across a range of readout durations and maximum temperatures for Cartesian, spiral-out, and retraced spiral-in/out (RIO) trajectories. The RIO trajectory was applied for stack-of-spirals 3D imaging on a real-time imaging platform and preliminary evaluation was carried out compared to a standard 2D sequence in vivo using a swine brain model, comparing maximum and mean temperatures measured between the two methods, as well as the temporal standard deviation measured by the two methods. In simulations, low-bandwidth Cartesian trajectories showed substantial shift of the focal spot, whereas both spiral trajectories showed no shift while maintaining focal spot geometry. In vivo, the 3D sequence achieved real-time 4D monitoring of thermometry, with an update time of 2.9-3.3 s. Spiral imaging, and RIO imaging in particular, is an effective way to speed up volumetric MR thermometry. Magn Reson Med 79:3122-3127, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Time-resolved echo-shared parallel MRA of the lung: observer preference study of image quality in comparison with non-echo-shared sequences

International Nuclear Information System (INIS)

Fink, C.; Puderbach, M.; Zaporozhan, J.; Plathow, C.; Kauczor, H.-U.; Ley, S.

2005-01-01

The aim of this study was to evaluate the image quality of time-resolved echo-shared parallel MRA of the lung. The pulmonary vasculature of nine patients (seven females, two males; median age: 44 years) with pulmonary disease was examined using a time-resolved MRA sequence combining echo sharing with parallel imaging (time-resolved echo-shared angiography technique, or TREAT). The sharpness of the vessel borders, conspicuousness of peripheral lung vessels, artifact level, and overall image quality of TREAT was assessed independently by four readers in a side-by-side comparison with non-echo-shared time-resolved parallel MRA data (pMRA) previously acquired in the same patients. Furthermore, the SNR of pulmonary arteries (PA) and veins (PV) achieved with both pulse sequences was compared. The mean voxel size of TREAT MRA was decreased by 24% compared with the non-echo-shared MRA. Regarding the sharpness of the vessel borders, conspicuousness of peripheral lung vessels, and overall image quality the TREAT sequence was rated superior in 75-76% of all cases. If the TREAT images were preferred over the pMRA images, the advantage was rated as major in 61-71% of all cases. The level of artifacts was not increased with the TREAT sequence. The mean interobserver agreement for all categories ranged between fair (artifact level) and good (overall image quality). The maximum SNR of TREAT did not differ from non-echo-shared parallel MRA (PA: TREAT: 273±45; pMRA: 280±71; PV: TREAT: 273±33; pMRA: 258±62). TREAT achieves a higher spatial resolution than non-echo-shared parallel MRA which is also perceived as an improved image quality. (orig.)

Exploring the effects of gravity on tongue motion using ultrasound image sequences

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Stone, Maureen; Crouse, Ulla; Sutton, Marty

2002-05-01

Our goal in the research was to explore the effect that gravity had on the vocal-tract system by using ultrasound data collected in the upright and supine positions. All potential subjects were given an ultrasound pretest to determine whether they could repeat a series of 3-4 words precise enough to allow an accurate series of images to be collected. Out of these potential subjects, approximately 5-7 subjects were eventually used in the research. The method of collecting ultrasound data required the immobilization of the patient by restraining their neck in a custom fitted neck restraint. The neck restraint held an ultrasound transducer positioned at a critical angle underneath the patients' lower jawbone, which served to reduce errors and increase image resolution. To accurately analyze the series of images collected from ultrasound imaging, the surfaces of the tongue were digitized and tongue motion was time-aligned across the upright and supine sequences. Comparisons between the upright and supine data were then made by using L2 norms to determine averages and differences regarding the behavior between the two positions. Curves and locations of the maximum and minimum differences will be discussed.

Multiplex, rapid and sensitive isothermal detection of nucleic-acid sequence by endonuclease restriction-mediated real-time multiple cross displacement amplification

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Yi eWang

2016-05-01

Full Text Available We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA, which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5’ end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labelled at the 5’ end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5’ end short sequences and their complementary sequences, which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 minutes, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.

Science.gov (United States)

Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

2016-01-01

We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

Diagnostic value of a new myocardial perfusion agent, teboroxime (SO 30,217), utilizing a rapid planar imaging protocol: Preliminary results

International Nuclear Information System (INIS)

Hendel, R.C.; McSherry, B.; Karimeddini, M.; Leppo, J.A.

1990-01-01

Technetium-99m-labeled agents have advantages over thallium-201 in terms of photon statistics, cost and clinical availability. They have been suggested as an alternative to thallium for myocardial perfusion imaging. Teboroxime is a new boronic acid adduct of technetium dioxime (BATO) compound that demonstrates favorable characteristics in preliminary studies. With use of a novel (seated) patient positioning technique and a rapid dynamic acquisition protocol, 30 patients underwent planar imaging with teboroxoime while at rest and after maximal treadmill exercise. Postexercise scans were completed in an average time (mean +/- SD) of 4.4 +/- 1.6 min, with 4.8 +/- 1.5 min for the views at rest. These results were compared with coronary arteriography or thallium scintigraphy after treadmill exercise, or both. Diagnostic agreement (abnormal versus normal) was present in 28 of the 30 patients (p less than 0.001). Regarding physiologic assessment as compared with thallium scintigraphy, the finding of infarction and ischemia was concordant in 89% and 86% of patients, respectively. This report describes the initial use of teboroxime with a rapid dynamic planar imaging technique, resulting in a high correlation with exercise thallium scintigraphy. Delayed postexercise images obtained 5 to 10 min after exercise demonstrated rapid disappearance of exercise-induced defects noted on the initial (0 to 5 min) postexercise views. The rapid differential washout with teboroxime has not been previously described and the possible clinical significance is discussed

TrueFisp versus HASTE sequences in 3T cine MRI: Evaluation of image quality during phonation in patients with velopharyngeal insufficiency

International Nuclear Information System (INIS)

Kulinna-Cosentini, Christiane; Czerny, Christian; Weber, Michael; Baumann, Arnulf; Sinko, Klaus

2016-01-01

To evaluate the image quality of two fast dynamic magnetic resonance imaging (MRI) sequences: True fast imaging with steady state precession (TrueFisp) was compared with half-Fourier acquired single turbo-spin-echo (HASTE) sequence for the characterization of velopharyngeal insufficiency (VPI) in repaired cleft palate patients. Twenty-two patients (10 female and 12 male; mean age, 17.7 ± 10.6 years; range, 9-31) with suspected VPI underwent 3-T MRI using TrueFisp and HASTE sequences. Imaging was performed in the sagittal plane at rest and during phonation of ''ee'' and ''k'' to assess the velum, tongue, posterior pharyngeal wall and a potential VP closure. The results were analysed independently by one radiologist and one orthodontist. HASTE performed better than TrueFisp for all evaluated items, except the tongue evaluation by the orthodontist during phonation of ''k'' and ''ee''. A statistically significant difference in favour of HASTE was observed in assessing the velum at rest and during phonation of ''k'' and ''ee'', and also in assessing VP closure in both raters (p < 0.05). TrueFisp imaging was twice as fast as HASTE (0.36 vs. 0.75 s/image). Dynamic HASTE images were of superior quality to those obtained with TrueFisp, although TrueFisp imaging was twice as fast. (orig.)

Comparison of single-use and reusable metal laryngoscope blades for orotracheal intubation during rapid sequence induction of anesthesia: a multicenter cluster randomized study.

Science.gov (United States)

Amour, Julien; Le Manach, Yannick Le; Borel, Marie; Lenfant, François; Nicolas-Robin, Armelle; Carillion, Aude; Ripart, Jacques; Riou, Bruno; Langeron, Olivier

2010-02-01

Single-use metal laryngoscope blades are cheaper and carry a lower risk of infection than reusable metal blades. The authors compared single-use and reusable metal blades during rapid sequence induction of anesthesia in a multicenter cluster randomized trial. One thousand seventy-two adult patients undergoing general anesthesia under emergency conditions and requiring rapid sequence induction were randomly assigned on a weekly basis to either single-use or reusable metal blades (cluster randomization). After induction, a 60-s period was allowed to complete intubation. In the case of failed intubation, a second attempt was performed using the opposite type of blade. The primary endpoint was the rate of failed intubation, and the secondary endpoints were the incidence of complications (oxygen desaturation, lung aspiration, and/or oropharynx trauma) and the Cormack and Lehane score. Both groups were similar in their main characteristics, including the risk factors for difficult intubation. The rate of failed intubation was significantly decreased with single-use metal blades at the first attempt compared with reusable blades (2.8 vs. 5.4%, P < 0.05). In addition, the proportion of grades III and IV in Cormack and Lehane score were also significantly decreased with single-use metal blades (6 vs. 10%, P < 0.05). The global complication rate did not reach statistical significance, although the same trend was noted (6.8% vs. 11.5%, P = not significant). An investigator survey and a measure of illumination pointed that illumination might have been responsible for this result. The single-use metal blade was more efficient than a reusable metal blade in rapid sequence induction of anesthesia.

Rapid-Sequence Intubation in the Left-Lateral Tilt Position in a Pregnant Woman with Premature Placental Abruption Utilizing a Videolaryngoscope

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Kenta Nakao

2015-04-01

Full Text Available Case - A 24-year-old pregnant woman was admitted to our hospital with decreased fetal heart rate. Obstetric examination revealed premature placental abruption; emergent caesarean section was planned under general anesthesia. On entering the operating room, the patient showed severe vital sign deterioration (blood pressure, 75/45 mm Hg; heart rate, 142 beats per minute. As left uterine displacement may worsen the premature placental abruption, the patient was placed in the left-lateral tilt position by rotating the operating table to release compression on the inferior vena cava by theuterus. To avoid circulatory collapse, rapid-sequence intubation was performed in this position. Tracheal intubation was performed with the Pentax-AWS Airwayscope (AWS videolaryngoscope, AWS; HOYA, Japan to obtain a good laryngeal view and minimize stress from laryngoscopy. After sufficient oxygenation, 120 mg of thiopental was administered. A second anesthesiologist performed cricoid pressure and 50 mg of rocuronium was administered after confirming loss of consciousness. This was followed by insertion of the AWS with a thin intlock into the mouth. Tracheal intubation was performed uneventfully. Discussion - Rapid-sequence intubation in the left-lateral tilted position with the AWS videolaryngoscope may be beneficial for pregnant women with vital sign deterioration.

Evaluation of pneumonia in children: comparison of MRI with fast imaging sequences at 1.5T with chest radiographs

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Yikilmaz, Ali; Koc, Ali; Coskun, Abdulhakim (Dept. of Radiology, Erciyes Medical School, Kayseri (Turkey)); Ozturk, Mustafa K (Dept. of Pediatric Infectious Diseases, Erciyes Medical School, Kayseri (Turkey)); Mulkern, Robert V; Lee, Edward Y (Dept. of Radiology and Dept. of Medicine, Pulmonary Div., Children' s Hospital Boston and Harvard Medical School, Boston (United States)), email: Edward.lee@childrens.harvard.edu

2011-10-15

Background Although there has been a study aimed at magnetic resonance imaging (MRI) evaluation of pneumonia in children at a low magnetic field (0.2T), there is no study which assessed the efficacy of MRI, particularly with fast imaging sequences at 1.5T, for evaluating pneumonia in children. Purpose To investigate the efficacy of chest MRI with fast imaging sequences at 1.5T for evaluating pneumonia in children by comparing MRI findings with those of chest radiographs. Material and Methods This was an Institutional Review Board-approved, HIPPA-compliant prospective study of 40 consecutive pediatric patients (24 boys, 16 girls; mean age 7.3 years +- 6.6 years) with pneumonia, who underwent PA and lateral chest radiographs followed by MRI within 24 h. All MRI studies were obtained in axial and coronal planes with two different fast imaging sequences: T1-weighted FFE (Fast Field Echo) (TR/TE: 83/4.6) and T2-weighted B-FFE M2D (Balanced Fast Field Echo Multiple 2D Dimensional) (TR/TE: 3.2/1.6). Two experienced pediatric radiologists reviewed each chest radiograph and MRI for the presence of consolidation, necrosis/abscess, bronchiectasis, and pleural effusion. Chest radiograph and MRI findings were compared with Kappa statistics. Results All consolidation, lung necrosis/abscess, bronchiectasis, and pleural effusion detected with chest radiographs were also detected with MRI. There was statistically substantial agreement between chest radiographs and MRI in detecting consolidation (k = 0.78) and bronchiectasis (k = 0.72) in children with pneumonia. The agreement between chest radiographs and MRI was moderate for detecting necrosis/abscess (k = 0.49) and fair for detecting pleural effusion (k = 0.30). Conclusion MRI with fast imaging sequences is comparable to chest radiographs for evaluating underlying pulmonary consolidation, bronchiectasis, necrosis/abscess, and pleural effusion often associated with pneumonia in children

Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

Science.gov (United States)

Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

2018-01-01

Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

Science.gov (United States)

Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

2018-05-01

Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

Magnetic resonance (MR) cine imaging of the human heart

International Nuclear Information System (INIS)

Waterton, J.C.

1985-01-01

A novel approach has been developed for MR cine imaging of the human heart by a modified ECG-gated 2DFT method. A pulse sequence has been devised to minimise the effects of saturation which can be anticipated in sequences that require rapid pulsing. Five frames are produced at the same anatomical level at predetermined intervals during the cardiac cycle. The total time taken to achieve this data is 8 minutes. Additional frames can be interleaved by repeating the sequence with an ECG-gated delay. The anatomical sections, which can be in any orthogonal plane, are then displayed as a cine loop. Cine display in the coronal plane has been used to examine 10 volunteers and 12 patients. In addition to the morphological feature displayed in single slice ECG-gated imaging, areas of dyskinesia can be detected and subjective estimates have been made of left ventricular function. (author)

gr-MRI: A software package for magnetic resonance imaging using software defined radios

Science.gov (United States)

Hasselwander, Christopher J.; Cao, Zhipeng; Grissom, William A.

2016-09-01

The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5 Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately 2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500 kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs.

Examination of self-navigating MR-sequences for perfusion imaging of the kidneys; Untersuchung von selbstnavigierenden MR-Sequenzen fuer die Perfusionsbildgebung der Nieren

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Lietzmann, Florian; Zoellner, Frank G.; Schad, Lothar R. [Heidelberg Univ. Medizinische Fakultaet Mannheim (Germany). Computerunterstuetzte Klinische Medizin; Michaely, Henrik J. [Heidelberg Univ. Medizinische Fakultaet Mannheim (Germany). Inst. fuer Klinische Radiologie und Nuklearmedizin

2010-07-01

Due to the worldwide increasing number of cases of chronic kidney diseases renal imaging - as a non-invasive technique in magnetic resonance imaging - has become a very important tool for an early diagnosis of probable insufficiencies and malfunction. Especially, dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) provides a technique to derive physiological parameters like renal blood flow or glomerular filtration rate. Similar to the entire field of abdominal imaging, the major problems are motion artifacts that primarily arise from the patient's respiration. The self-navigating BLADE-sequence with a post processing motion correction is an approach that does not require breath holding and is therefore also easily applicable to patients who are not able to undergo multiple breath hold examinations. In this work, a T1-weighted BLADE-sequence was optimized to demonstrate the feasibility of this technique to perfusion imaging. The number of phase-encoding lines of one BLADE has a direct impact on the reduction of motion artifacts. In comparison to standard DCE-MRI sequences, the developed BLADE-sequence with optimized number of phase encoding lines could significantly reduce motion artifacts. A quantitative analysis revealed that up to a 50% displacement of the kidneys could be corrected. Therefore, it was demonstrated that dynamic motion corrected measurements without the need of a breath hold-technique are feasible. (orig.)

Easy Leaf Area: Automated Digital Image Analysis for Rapid and Accurate Measurement of Leaf Area

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Hsien Ming Easlon

2014-07-01

Full Text Available Premise of the study: Measurement of leaf areas from digital photographs has traditionally required significant user input unless backgrounds are carefully masked. Easy Leaf Area was developed to batch process hundreds of Arabidopsis rosette images in minutes, removing background artifacts and saving results to a spreadsheet-ready CSV file. Methods and Results: Easy Leaf Area uses the color ratios of each pixel to distinguish leaves and calibration areas from their background and compares leaf pixel counts to a red calibration area to eliminate the need for camera distance calculations or manual ruler scale measurement that other software methods typically require. Leaf areas estimated by this software from images taken with a camera phone were more accurate than ImageJ estimates from flatbed scanner images. Conclusions: Easy Leaf Area provides an easy-to-use method for rapid measurement of leaf area and nondestructive estimation of canopy area from digital images.

A new feedback image encryption scheme based on perturbation with dynamical compound chaotic sequence cipher generator

Science.gov (United States)

Tong, Xiaojun; Cui, Minggen; Wang, Zhu

2009-07-01

The design of the new compound two-dimensional chaotic function is presented by exploiting two one-dimensional chaotic functions which switch randomly, and the design is used as a chaotic sequence generator which is proved by Devaney's definition proof of chaos. The properties of compound chaotic functions are also proved rigorously. In order to improve the robustness against difference cryptanalysis and produce avalanche effect, a new feedback image encryption scheme is proposed using the new compound chaos by selecting one of the two one-dimensional chaotic functions randomly and a new image pixels method of permutation and substitution is designed in detail by array row and column random controlling based on the compound chaos. The results from entropy analysis, difference analysis, statistical analysis, sequence randomness analysis, cipher sensitivity analysis depending on key and plaintext have proven that the compound chaotic sequence cipher can resist cryptanalytic, statistical and brute-force attacks, and especially it accelerates encryption speed, and achieves higher level of security. By the dynamical compound chaos and perturbation technology, the paper solves the problem of computer low precision of one-dimensional chaotic function.

Rapid intracerebroventricular delivery of Cu-DOTA-etanercept after peripheral administration demonstrated by PET imaging

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Chen Xiaoyuan

2009-02-01

Full Text Available Abstract Background The cytokines interleukin-1 and tumor necrosis factor (TNF, and the cytokine blocker interleukin-1 receptor antagonist, all have been demonstrated to enter the cerebrospinal fluid (CSF following peripheral administration. Recent reports of rapid clinical improvement in patients with Alzheimer's disease and related forms of dementia following perispinal administration of etanercept, a TNF antagonist, suggest that etanercept also has the ability to reach the brain CSF. To investigate, etanercept was labeled with a positron emitter to enable visualization of its intracranial distribution following peripheral administration by PET in an animal model. Findings Radiolabeling of etanercept with the PET emitter 64Cu was performed by DOTA (1,4,7,10-tetraazadodecane-N,N',N",N"'-tetraacetic acid conjugation of etanercept, followed by column purification and 64Cu labeling. MicroPET imaging revealed accumulation of 64Cu-DOTA-etanercept within the lateral and third cerebral ventricles within minutes of peripheral perispinal administration in a normal rat anesthesized with isoflurane anesthesia, with concentration within the choroid plexus and into the CSF. Conclusion Synthesis of 64Cu-DOTA-etanercept enabled visualization of its intracranial distribution by microPET imaging. MicroPET imaging documented rapid accumulation of 64Cu-DOTA-etanercept within the choroid plexus and the cerebrospinal fluid within the cerebral ventricles of a living rat after peripheral administration. Further study of the effects of etanercept and TNF at the level of the choroid plexus may yield valuable insights into the pathogenesis of Alzheimer's disease.

A rapid method for creating qualitative images indicative of thick oil emulsion on the ocean's surface from imaging spectrometer data

Science.gov (United States)

Kokaly, Raymond F.; Hoefen, Todd M.; Livo, K. Eric; Swayze, Gregg A.; Leifer, Ira; McCubbin, Ian B.; Eastwood, Michael L.; Green, Robert O.; Lundeen, Sarah R.; Sarture, Charles M.; Steele, Denis; Ryan, Thomas; Bradley, Eliza S.; Roberts, Dar A.; ,

2010-01-01

This report describes a method to create color-composite images indicative of thick oil:water emulsions on the surface of clear, deep ocean water by using normalized difference ratios derived from remotely sensed data collected by an imaging spectrometer. The spectral bands used in the normalized difference ratios are located in wavelength regions where the spectra of thick oil:water emulsions on the ocean's surface have a distinct shape compared to clear water and clouds. In contrast to quantitative analyses, which require rigorous conversion to reflectance, the method described is easily computed and can be applied rapidly to radiance data or data that have been atmospherically corrected or ground-calibrated to reflectance. Examples are shown of the method applied to Airborne Visible/Infrared Imaging Spectrometer data collected May 17 and May 19, 2010, over the oil spill from the Deepwater Horizon offshore oil drilling platform in the Gulf of Mexico.

Statistical intensity variation analysis for rapid volumetric imaging of capillary network flux.

Science.gov (United States)

Lee, Jonghwan; Jiang, James Y; Wu, Weicheng; Lesage, Frederic; Boas, David A

2014-04-01

We present a novel optical coherence tomography (OCT)-based technique for rapid volumetric imaging of red blood cell (RBC) flux in capillary networks. Previously we reported that OCT can capture individual RBC passage within a capillary, where the OCT intensity signal at a voxel fluctuates when an RBC passes the voxel. Based on this finding, we defined a metric of statistical intensity variation (SIV) and validated that the mean SIV is proportional to the RBC flux [RBC/s] through simulations and measurements. From rapidly scanned volume data, we used Hessian matrix analysis to vectorize a segment path of each capillary and estimate its flux from the mean of the SIVs gathered along the path. Repeating this process led to a 3D flux map of the capillary network. The present technique enabled us to trace the RBC flux changes over hundreds of capillaries with a temporal resolution of ~1 s during functional activation.

Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples.

Science.gov (United States)

Borsu, Laetitia; Intrieri, Julie; Thampi, Linta; Yu, Helena; Riely, Gregory; Nafa, Khedoudja; Chandramohan, Raghu; Ladanyi, Marc; Arcila, Maria E

2016-11-01

Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Passive IFF: Autonomous Nonintrusive Rapid Identification of Friendly Assets

Science.gov (United States)

Moynihan, Philip; Steenburg, Robert Van; Chao, Tien-Hsin

2004-01-01

A proposed optoelectronic instrument would identify targets rapidly, without need to radiate an interrogating signal, apply identifying marks to the targets, or equip the targets with transponders. The instrument was conceived as an identification, friend or foe (IFF) system in a battlefield setting, where it would be part of a targeting system for weapons, by providing rapid identification for aimed weapons to help in deciding whether and when to trigger them. The instrument could also be adapted to law-enforcement and industrial applications in which it is necessary to rapidly identify objects in view. The instrument would comprise mainly an optical correlator and a neural processor (see figure). The inherent parallel-processing speed and capability of the optical correlator would be exploited to obtain rapid identification of a set of probable targets within a scene of interest and to define regions within the scene for the neural processor to analyze. The neural processor would then concentrate on each region selected by the optical correlator in an effort to identify the target. Depending on whether or not a target was recognized by comparison of its image data with data in an internal database on which the neural processor was trained, the processor would generate an identifying signal (typically, friend or foe ). The time taken for this identification process would be less than the time needed by a human or robotic gunner to acquire a view of, and aim at, a target. An optical correlator that has been under development for several years and that has been demonstrated to be capable of tracking a cruise missile might be considered a prototype of the optical correlator in the proposed IFF instrument. This optical correlator features a 512-by-512-pixel input image frame and operates at an input frame rate of 60 Hz. It includes a spatial light modulator (SLM) for video-to-optical image conversion, a pair of precise lenses to effect Fourier transforms, a filter SLM

Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae, a mammalian family that experienced rapid speciation

Directory of Open Access Journals (Sweden)

Ryder Oliver A

2007-10-01

Full Text Available Abstract Background Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family represents a typical example of rapid evolutionary radiation. Previous analyses with a single mitochondrial (mt gene or a small number of mt genes either provide weak support or a large unresolved polytomy for ursids. We revisit the contentious relationships within Ursidae by analyzing complete mt genome sequences and evaluating the performance of both entire mt genomes and constituent mtDNA genes in recovering a phylogeny of extremely recent speciation events. Results This mitochondrial genome-based phylogeny provides strong evidence that the spectacled bear diverged first, while within the genus Ursus, the sloth bear is the sister taxon of all the other five ursines. The latter group is divided into the brown bear/polar bear and the two black bears/sun bear assemblages. These findings resolve the previous conflicts between trees using partial mt genes. The ability of different categories of mt protein coding genes to recover the correct phylogeny is concordant with previous analyses for taxa with deep divergence times. This study provides a robust Ursidae phylogenetic framework for future validation by additional independent evidence, and also has significant implications for assisting in the resolution of other similarly difficult phylogenetic investigations. Conclusion Identification of base composition bias and utilization of the combined data of whole mitochondrial genome sequences has allowed recovery of a strongly supported phylogeny that is upheld when using multiple alternative outgroups for the Ursidae, a mammalian family that underwent a rapid radiation since the mid- to late Pliocene. It remains to be seen if the reliability of mt genome analysis will hold up in studies of other

Statistical approach of measurement of signal to noise ratio in according to change pulse sequence on brain MRI meningioma and cyst images

International Nuclear Information System (INIS)

Lee, Eul Kyu; Choi, Kwan Woo; Jeong, Hoi Woun; Jang, Seo Goo; Kim, Ki Won; Son, Soon Yong; Min, Jung Whan; Son, Jin Hyun

2016-01-01

The purpose of this study was to needed basis of measure MRI CAD development for signal to noise ratio (SNR) by pulse sequence analysis from region of interest (ROI) in brain magnetic resonance imaging (MRI) contrast. We examined images of brain MRI contrast enhancement of 117 patients, from January 2005 to December 2015 in a University-affiliated hospital, Seoul, Korea. Diagnosed as one of two brain diseases such as meningioma and cysts SNR for each patient's image of brain MRI were calculated by using Image J. Differences of SNR among two brain diseases were tested by SPSS Statistics21 ANOVA test for there was statistical significance (p < 0.05). We have analysis socio-demographical variables, SNR according to sequence disease, 95% confidence according to SNR of sequence and difference in a mean of SNR. Meningioma results, with the quality of distributions in the order of T1CE, T2 and T1, FLAIR. Cysts results, with the quality of distributions in the order of T2 and T1, T1CE and FLAIR. SNR of MRI sequences of the brain would be useful to classify disease. Therefore, this study will contribute to evaluate brain diseases, and be a fundamental to enhancing the accuracy of CAD development

Statistical approach of measurement of signal to noise ratio in according to change pulse sequence on brain MRI meningioma and cyst images

Energy Technology Data Exchange (ETDEWEB)

Lee, Eul Kyu [Inje Paik University Hospital Jeo-dong, Seoul (Korea, Republic of); Choi, Kwan Woo [Asan Medical Center, Seoul (Korea, Republic of); Jeong, Hoi Woun [The Baekseok Culture University, Cheonan (Korea, Republic of); Jang, Seo Goo [The Soonchunhyang University, Asan (Korea, Republic of); Kim, Ki Won [Kyung Hee University Hospital at Gang-dong, Seoul (Korea, Republic of); Son, Soon Yong [The Wonkwang Health Science University, Iksan (Korea, Republic of); Min, Jung Whan; Son, Jin Hyun [The Shingu University, Sungnam (Korea, Republic of)

2016-09-15

The purpose of this study was to needed basis of measure MRI CAD development for signal to noise ratio (SNR) by pulse sequence analysis from region of interest (ROI) in brain magnetic resonance imaging (MRI) contrast. We examined images of brain MRI contrast enhancement of 117 patients, from January 2005 to December 2015 in a University-affiliated hospital, Seoul, Korea. Diagnosed as one of two brain diseases such as meningioma and cysts SNR for each patient's image of brain MRI were calculated by using Image J. Differences of SNR among two brain diseases were tested by SPSS Statistics21 ANOVA test for there was statistical significance (p < 0.05). We have analysis socio-demographical variables, SNR according to sequence disease, 95% confidence according to SNR of sequence and difference in a mean of SNR. Meningioma results, with the quality of distributions in the order of T1CE, T2 and T1, FLAIR. Cysts results, with the quality of distributions in the order of T2 and T1, T1CE and FLAIR. SNR of MRI sequences of the brain would be useful to classify disease. Therefore, this study will contribute to evaluate brain diseases, and be a fundamental to enhancing the accuracy of CAD development.

Comparison of a T1-weighted inversion-recovery-, gradient-echo- and spin-echo sequence for imaging of the brain at 3.0 Tesla

International Nuclear Information System (INIS)

Stehling, C.; Niederstadt, T.; Kraemer, S.; Kugel, H.; Schwindt, W.; Heindel, W.; Bachmann, R.

2005-01-01

Purpose: The increased T1 relaxation times at 3.0 Tesla lead to a reduced T1 contrast, requiring adaptation of imaging protocols for high magnetic fields. This prospective study assesses the performance of three techniques for T1-weighted imaging (T1w) at 3.0 T with regard to gray-white differentiation and contrast-to-noise-ratio (CNR). Materials and Methods: Thirty-one patients were examined at a 3.0 T system with axial T1 w inversion recovery (IR), spin-echo (SE) and gradient echo (GE) sequences and after contrast enhancement (CE) with CE-SE and CE-GE sequences. For qualitative analysis, the images were ranked with regard to artifacts, gray-white differentiation, image noise and overall diagnostic quality. For quantitative analysis, the CNR was calculated, and cortex and basal ganglia were compared with the white matter. Results: In the qualitative analysis, IR was judged superior to SE and GE for gray-white differentiation, image noise and overall diagnostic quality, but inferior to the GE sequence with regard to artifacts. CE-GE proved superior to CE-SE in all categories. In the quantitative analysis, CNR of the based ganglia was highest for IR, followed by GE and SE. For the CNR of the cortex, no significant difference was found between IR (16.9) and GE (15.4) but both were superior to the SE (9.4). The CNR of the cortex was significantly higher for CE-GE compared to CE-SE (12.7 vs. 7.6, p<0.001), but the CNR of the basal ganglia was not significantly different. Conclusion: For unenhanced T1w imaging at 3.0 T, the IR technique is, despite increased artifacts, the method of choice due to its superior gray-white differentiation and best overall image quality. For CE-studies, GE sequences are recommended. For cerebral imaging, SE sequences give unsatisfactory results at 3.0 T. (orig.)

SU-E-I-51: Use of Blade Sequences in Cervical Spine MR Imaging for Eliminating Motion, Truncation and Flow Artifacts

Energy Technology Data Exchange (ETDEWEB)

Mavroidis, P [University of Texas Health Science Center, UTHSCSA, San Antonio, TX (United States); Lavdas, E; Kostopoulos, S; Ninos, C; Strikou, A; Glotsos, D; Vlachopoulou, A; Oikonomou, G [Technological Education Institute of Athens, Athens, Athens (Greece); Economopoulos, N [General University Hospital ATTIKON, Athens, Athens (Greece); Roka, V [Health Center of Farkadona, Trikala (Greece); Sakkas, G [Center for Research and Technology of Thessaly, Trikala (Greece); Tsagkalis, A; Batsikas, G [IASO Thessalias Hospital, Larissa (Greece); Statkahis, S [Cancer Therapy and Research Center, San Antonio, TX (United States); Papanikolaou, N [University of Texas HSC SA, San Antonio, TX (United States)

2014-06-01

Purpose: To assess the efficacy of the BLADE technique to eliminate motion, truncation, flow and other artifacts in Cervical Spine MRI compared to the conventional technique. To study the ability of the examined sequences to reduce the indetention and wrap artifacts, which have been reported in BLADE sagittal sequences. Methods: Forty consecutive subjects, who had been routinely scanned for cervical spine examination using four different image acquisition techniques, were analyzed. More specifically, the following pairs of sequences were compared: a) T2 TSE SAG vs. T2 TSE SAG BLADE and b) T2 TIRM SAG vs. T2 TIRM SAG BLADE. A quantitative analysis was performed using the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and relative contrast (ReCon) measures. A qualitative analysis was also performed by two radiologists, who graded seven image characteristics on a 5-point scale (0:non-visualization; 1:poor; 2:average; 3:good; 4:excellent). The observers also evaluated the presence of image artifacts (motion, truncation, flow, indentation). Results: Based on the findings of the quantitative analysis, the ReCON values of the CSF (cerebrospinal fluid)/SC (spinal cord) between TIRM SAG and TIRM SAG BLADE were found to present statistical significant differences (p<0.001). Regarding motion and truncation artifacts, the T2 TSE SAG BLADE was superior compared to the T2 TSE SAG and the T2 TIRM SAG BLADE was superior compared to the T2 TIRM SAG. Regarding flow artifacts, T2 TIRM SAG BLADE eliminated more artifacts compared to the T2 TIRM SAG. Conclusion: The use of BLADE sequences in cervical spine MR examinations appears to be capable of potentially eliminating motion, pulsatile flow and trancation artifacts. Furthermore, BLADE sequences are proposed to be used in the standard examination protocols based on the fact that a significantly improved image quality could be achieved.

SU-E-I-51: Use of Blade Sequences in Cervical Spine MR Imaging for Eliminating Motion, Truncation and Flow Artifacts

International Nuclear Information System (INIS)

Mavroidis, P; Lavdas, E; Kostopoulos, S; Ninos, C; Strikou, A; Glotsos, D; Vlachopoulou, A; Oikonomou, G; Economopoulos, N; Roka, V; Sakkas, G; Tsagkalis, A; Batsikas, G; Statkahis, S; Papanikolaou, N

2014-01-01

Purpose: To assess the efficacy of the BLADE technique to eliminate motion, truncation, flow and other artifacts in Cervical Spine MRI compared to the conventional technique. To study the ability of the examined sequences to reduce the indetention and wrap artifacts, which have been reported in BLADE sagittal sequences. Methods: Forty consecutive subjects, who had been routinely scanned for cervical spine examination using four different image acquisition techniques, were analyzed. More specifically, the following pairs of sequences were compared: a) T2 TSE SAG vs. T2 TSE SAG BLADE and b) T2 TIRM SAG vs. T2 TIRM SAG BLADE. A quantitative analysis was performed using the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and relative contrast (ReCon) measures. A qualitative analysis was also performed by two radiologists, who graded seven image characteristics on a 5-point scale (0:non-visualization; 1:poor; 2:average; 3:good; 4:excellent). The observers also evaluated the presence of image artifacts (motion, truncation, flow, indentation). Results: Based on the findings of the quantitative analysis, the ReCON values of the CSF (cerebrospinal fluid)/SC (spinal cord) between TIRM SAG and TIRM SAG BLADE were found to present statistical significant differences (p<0.001). Regarding motion and truncation artifacts, the T2 TSE SAG BLADE was superior compared to the T2 TSE SAG and the T2 TIRM SAG BLADE was superior compared to the T2 TIRM SAG. Regarding flow artifacts, T2 TIRM SAG BLADE eliminated more artifacts compared to the T2 TIRM SAG. Conclusion: The use of BLADE sequences in cervical spine MR examinations appears to be capable of potentially eliminating motion, pulsatile flow and trancation artifacts. Furthermore, BLADE sequences are proposed to be used in the standard examination protocols based on the fact that a significantly improved image quality could be achieved

A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

OpenAIRE

Farkhondeh Saba; Moslem Papizadeh; Javad Khansha; Mahshid Sedghi; Mehrnoosh Rasooli; Mohammad Ali Amoozegar; Mohammad Reza Soudi; Seyed Abolhassan Shahzadeh Fazeli

2016-01-01

Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR). Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Me...

Can a single-shot black-blood T2-weighted spin-echo echo-planar imaging sequence with sensitivity encoding replace the respiratory-triggered turbo spin-echo sequence for the liver? An optimization and feasibility study.

Science.gov (United States)

Hussain, Shahid M; De Becker, Jan; Hop, Wim C J; Dwarkasing, Soendersing; Wielopolski, Piotr A

2005-03-01

To optimize and assess the feasibility of a single-shot black-blood T2-weighted spin-echo echo-planar imaging (SSBB-EPI) sequence for MRI of the liver using sensitivity encoding (SENSE), and compare the results with those obtained with a T2-weighted turbo spin-echo (TSE) sequence. Six volunteers and 16 patients were scanned at 1.5T (Philips Intera). In the volunteer study, we optimized the SSBB-EPI sequence by interactively changing the parameters (i.e., the resolution, echo time (TE), diffusion weighting with low b-values, and polarity of the phase-encoding gradient) with regard to distortion, suppression of the blood signal, and sensitivity to motion. The influence of each change was assessed. The optimized SSBB-EPI sequence was applied in patients (N = 16). A number of items, including the overall image quality (on a scale of 1-5), were used for graded evaluation. In addition, the signal-to-noise ratio (SNR) of the liver was calculated. Statistical analysis was carried out with the use of Wilcoxon's signed rank test for comparison of the SSBB-EPI and TSE sequences, with P = 0.05 considered the limit for significance. The SSBB-EPI sequence was improved by the following steps: 1) less frequency points than phase-encoding steps, 2) a b-factor of 20, and 3) a reversed polarity of the phase-encoding gradient. In patients, the mean overall image quality score for the optimized SSBB-EPI (3.5 (range: 1-4)) and TSE (3.6 (range: 3-4)), and the SNR of the liver on SSBB-EPI (mean +/- SD = 7.6 +/- 4.0) and TSE (8.9 +/- 4.6) were not significantly different (P > .05). Optimized SSBB-EPI with SENSE proved to be feasible in patients, and the overall image quality and SNR of the liver were comparable to those achieved with the standard respiratory-triggered T2-weighted TSE sequence. (c) 2005 Wiley-Liss, Inc.

Sequencing of the Chlamydophila psittaci ompA Gene Reveals a New Genotype, E/B, and the Need for a Rapid Discriminatory Genotyping Method

Science.gov (United States)

Geens, Tom; Desplanques, Ann; Van Loock, Marnix; Bönner, Brigitte M.; Kaleta, Erhard F.; Magnino, Simone; Andersen, Arthur A.; Everett, Karin D. E.; Vanrompay, Daisy

2005-01-01

Twenty-one avian Chlamydophila psittaci isolates from different European countries were characterized using ompA restriction fragment length polymorphism, ompA sequencing, and major outer membrane protein serotyping. Results reveal the presence of a new genotype, E/B, in several European countries and stress the need for a discriminatory rapid genotyping method. PMID:15872282

Rapid musculoskeletal magnetic resonance imaging using integrated parallel acquisition techniques (IPAT) - Initial experiences

Energy Technology Data Exchange (ETDEWEB)

Romaneehsen, B.; Oberholzer, K.; Kreitner, K.-F. [Johannes Gutenberg-Univ. Mainz (Germany). Klinik und Poliklinik fuer Radiologie; Mueller, L.P. [Johannes Gutenberg-Univ. Mainz (Germany). Klinik und Poliklinik fuer Unfallchirurgie

2003-09-01

Purpose: To investigate the feasibility of using multiple receiver coil elements for time saving integrated parallel imaging techniques (iPAT) in traumatic musculoskeletal disorders. Material and methods: 6 patients with traumatic derangements of the knee, ankle and hip underwent MR imaging at 1.5 T. For signal detection of the knee and ankle, we used a 6-channel body array coil that was placed around the joints, for hip imaging two 4-channel body array coils and two elements of the spine array coil were combined for signal detection. All patients were investigated with a standard imaging protocol that mainly consisted of different turbo spin-echo sequences (PD-, T{sub 2}-weighted TSE with and without fat suppression, STIR). All sequences were repeated with an integrated parallel acquisition technique (iPAT) using a modified sensitivity encoding (mSENSE) technique with an acceleration factor of 2. Overall image quality was subjectively assessed using a five-point scale as well as the ability for detection of pathologic findings. Results: Regarding overall image quality, there were no significant differences between standard imaging and imaging using mSENSE. All pathologies (occult fracture, meniscal tear, torn and interpositioned Hoffa's cleft, cartilage damage) were detected by both techniques. iPAT led to a 48% reduction of acquisition time compared with standard technique. Additionally, time savings with iPAT led to a decrease of pain-induced motion artifacts in two cases. Conclusion: In times of increasing cost pressure, iPAT using multiple coil elements seems to be an efficient and economic tool for fast musculoskeletal imaging with diagnostic performance comparable to conventional techniques. (orig.) [German] Ziel: Einsatz integrierter paralleler Akquisitionstechniken (iPAT) zur Verkuerzung der Untersuchungszeit bei muskuloskelettalen Verletzungen. Material und Methoden: 6 Patienten mit einem Knie, Sprunggelenks- oder Huefttrauma wurden bei 1,5 T

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

Science.gov (United States)

Kisand, Veljo; Lettieri, Teresa

2013-04-01

De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize

Comparing an accelerated 3D fast spin-echo sequence (CS-SPACE) for knee 3-T magnetic resonance imaging with traditional 3D fast spin-echo (SPACE) and routine 2D sequences

Energy Technology Data Exchange (ETDEWEB)

Altahawi, Faysal F.; Blount, Kevin J.; Omar, Imran M. [Northwestern University Feinberg School of Medicine, Department of Radiology, Chicago, IL (United States); Morley, Nicholas P. [Marshfield Clinic, Department of Radiology, Marshfield, WI (United States); Raithel, Esther [Siemens Healthcare GmbH, Erlangen (Germany)

2017-01-15

To compare a faster, new, high-resolution accelerated 3D-fast-spin-echo (3D-FSE) acquisition sequence (CS-SPACE) to traditional 2D and high-resolution 3D sequences for knee 3-T magnetic resonance imaging (MRI). Twenty patients received knee MRIs that included routine 2D (T1, PD ± FS, T2-FS; 0.5 x 0.5 x 3 mm{sup 3}; ∝10 min), traditional 3D FSE (SPACE-PD-FS; 0.5 x 0.5 x 0.5 mm{sup 3}; ∝7.5 min), and accelerated 3D-FSE prototype (CS-SPACE-PD-FS; 0.5 x 0.5 x 0.5 mm{sup 3}; ∝5 min) acquisitions on a 3-T MRI system (Siemens MAGNETOM Skyra). Three musculoskeletal radiologists (MSKRs) prospectively and independently reviewed the studies with graded surveys comparing image and diagnostic quality. Tissue-specific signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) were also compared. MSKR-perceived diagnostic quality of cartilage was significantly higher for CS-SPACE than for SPACE and 2D sequences (p < 0.001). Assessment of diagnostic quality of menisci and synovial fluid was higher for CS-SPACE than for SPACE (p < 0.001). CS-SPACE was not significantly different from SPACE but had lower assessments than 2D sequences for evaluation of bones, ligaments, muscles, and fat (p ≤ 0.004). 3D sequences had higher spatial resolution, but lower overall assessed contrast (p < 0.001). Overall image quality from CS-SPACE was assessed as higher than SPACE (p = 0.007), but lower than 2D sequences (p < 0.001). Compared to SPACE, CS-SPACE had higher fluid SNR and CNR against all other tissues (all p < 0.001). The CS-SPACE prototype allows for faster isotropic acquisitions of knee MRIs over currently used protocols. High fluid-to-cartilage CNR and higher spatial resolution over routine 2D sequences may present a valuable role for CS-SPACE in the evaluation of cartilage and menisci. (orig.)

Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

Energy Technology Data Exchange (ETDEWEB)

Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

2015-07-01

To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.

Science.gov (United States)

Ma, Peng-Fei; Guo, Zhen-Hua; Li, De-Zhu

2012-01-01

Compared to their counterparts in animals, the mitochondrial (mt) genomes of angiosperms exhibit a number of unique features. However, unravelling their evolution is hindered by the few completed genomes, of which are essentially Sanger sequenced. While next-generation sequencing technologies have revolutionized chloroplast genome sequencing, they are just beginning to be applied to angiosperm mt genomes. Chloroplast genomes of grasses (Poaceae) have undergone episodic evolution and the evolutionary rate was suggested to be correlated between chloroplast and mt genomes in Poaceae. It is interesting to investigate whether correlated rate change also occurred in grass mt genomes as expected under lineage effects. A time-calibrated phylogenetic tree is needed to examine rate change. We determined a largely completed mt genome from a bamboo, Ferrocalamus rimosivaginus (Poaceae), through Illumina sequencing of total DNA. With combination of de novo and reference-guided assembly, 39.5-fold coverage Illumina reads were finally assembled into scaffolds totalling 432,839 bp. The assembled genome contains nearly the same genes as the completed mt genomes in Poaceae. For examining evolutionary rate in grass mt genomes, we reconstructed a phylogenetic tree including 22 taxa based on 31 mt genes. The topology of the well-resolved tree was almost identical to that inferred from chloroplast genome with only minor difference. The inconsistency possibly derived from long branch attraction in mtDNA tree. By calculating absolute substitution rates, we found significant rate change (∼4-fold) in mt genome before and after the diversification of Poaceae both in synonymous and nonsynonymous terms. Furthermore, the rate change was correlated with that of chloroplast genomes in grasses. Our result demonstrates that it is a rapid and efficient approach to obtain angiosperm mt genome sequences using Illumina sequencing technology. The parallel episodic evolution of mt and chloroplast

Breast MRI at very short TE (minTE). Image analysis of minTE sequences on non-fat-saturated, subtracted T1-weighted images

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Wenkel, Evelyn; Janka, Rolf; Kaemmerer, Nadine; Uder, Michael; Hammon, Matthias; Brand, Michael [Univ. Hospital Erlangen (Germany). Dept. of Radiology; Geppert, Christian [Siemens Healthcare GmbH, Erlangen (Germany); Hartmann, Arndt [Univ. Hospital Erlangen (Germany). Dept. of Pathology

2017-02-15

The aim was to evaluate a minimum echo time (minTE) protocol for breast magnetic resonance imaging (MRI) in patients with breast lesions compared to a standard TE (nTE) time protocol. Breasts of 144 women were examined with a 1.5 Tesla MRI scanner. Additionally to the standard gradient-echo sequence with nTE (4.8 ms), a variant with minimum TE (1.2 ms) was used in an interleaved fashion which leads to a better temporal resolution and should reduce the scan time by approximately 50%. Lesion sizes were measured and the signal-to-noise ratio (SNR) as well as the contrast-to-noise ratio (CNR) were calculated. Subjective confidence was evaluated using a 3-point scale before looking at the nTE sequences (1 = very sure that I can identify a lesion and classify it, 2 = quite sure that I can identify a lesion and classify it, 3 = definitely want to see nTE for final assessment) and the subjective image quality of all examinations was evaluated using a four-grade scale (1 = sharp, 2 = slight blur, 3 = moderate blur and 4 = severe blur/not evaluable) for lesion and skin sharpness. Lesion morphology and contrast enhancement were also evaluated. With minTE sequences, no lesion was rated with ''definitely want to see nTE sequences for final assessment''. The difference of the longitudinal and transverse diameter did not differ significantly (p>0.05). With minTE, lesions and skin were rated to be significantly more blurry (p<0.01 for lesions and p<0.05 for skin). There was no difference between both sequences with respect to SNR, CNR, lesion morphology, contrast enhancement and detection of multifocal disease. Dynamic breast MRI with a minTE protocol is feasible without a major loss of information (SNR, CNR, lesion morphology, contrast enhancement and lesion sizes) and the temporal resolution can be increased by a factor of 2 using minTE sequences.

Breast MRI at very short TE (minTE). Image analysis of minTE sequences on non-fat-saturated, subtracted T1-weighted images

International Nuclear Information System (INIS)

Wenkel, Evelyn; Janka, Rolf; Kaemmerer, Nadine; Uder, Michael; Hammon, Matthias; Brand, Michael; Hartmann, Arndt

2017-01-01

The aim was to evaluate a minimum echo time (minTE) protocol for breast magnetic resonance imaging (MRI) in patients with breast lesions compared to a standard TE (nTE) time protocol. Breasts of 144 women were examined with a 1.5 Tesla MRI scanner. Additionally to the standard gradient-echo sequence with nTE (4.8 ms), a variant with minimum TE (1.2 ms) was used in an interleaved fashion which leads to a better temporal resolution and should reduce the scan time by approximately 50%. Lesion sizes were measured and the signal-to-noise ratio (SNR) as well as the contrast-to-noise ratio (CNR) were calculated. Subjective confidence was evaluated using a 3-point scale before looking at the nTE sequences (1 = very sure that I can identify a lesion and classify it, 2 = quite sure that I can identify a lesion and classify it, 3 = definitely want to see nTE for final assessment) and the subjective image quality of all examinations was evaluated using a four-grade scale (1 = sharp, 2 = slight blur, 3 = moderate blur and 4 = severe blur/not evaluable) for lesion and skin sharpness. Lesion morphology and contrast enhancement were also evaluated. With minTE sequences, no lesion was rated with ''definitely want to see nTE sequences for final assessment''. The difference of the longitudinal and transverse diameter did not differ significantly (p>0.05). With minTE, lesions and skin were rated to be significantly more blurry (p<0.01 for lesions and p<0.05 for skin). There was no difference between both sequences with respect to SNR, CNR, lesion morphology, contrast enhancement and detection of multifocal disease. Dynamic breast MRI with a minTE protocol is feasible without a major loss of information (SNR, CNR, lesion morphology, contrast enhancement and lesion sizes) and the temporal resolution can be increased by a factor of 2 using minTE sequences.

Surface coil imaging of the spine using fast sequences: Improvement of intensity profile and contrast behavior

International Nuclear Information System (INIS)

Requardt, H.; Deimling, M.; Weber, H.

1986-01-01

Sagittal and axial images obtained using a surface coil suffer from the extreme intensity profile caused by physical properties of the coil and the anatomic entity of subcutaneous fat. The authors present a measuring device that reduces these disadvantages by means of Helmholtz-type coils, and sequences that reduce the fat signal by dephasing its signal part. The extremely short repetition time (<30 msec) allows acquisition times shorter than 10 sec. Breath-holding for this short period to avoid movement artifacts is possible. Images are presented that illustrate the enhanced contrast of spinal tissue and surrounding structures. Comparisons are made with spin-echo and CHESS images

Improved imaging of cochlear nerve hypoplasia using a 3-Tesla variable flip-angle turbo spin-echo sequence and a 7-cm surface coil.

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Giesemann, Anja M; Raab, Peter; Lyutenski, Stefan; Dettmer, Sabine; Bültmann, Eva; Frömke, Cornelia; Lenarz, Thomas; Lanfermann, Heinrich; Goetz, Friedrich

2014-03-01

Magnetic resonance imaging of the temporal bone has an important role in decision making with regard to cochlea implantation, especially in children with cochlear nerve deficiency. The purpose of this study was to evaluate the usefulness of the combination of an advanced high-resolution T2-weighted sequence with a surface coil in a 3-Tesla magnetic resonance imaging scanner in cases of suspected cochlear nerve aplasia. Prospective study. Seven patients with cochlear nerve hypoplasia or aplasia were prospectively examined using a high-resolution three-dimensional variable flip-angle turbo spin-echo sequence using a surface coil, and the images were compared with the same sequence in standard resolution using a standard head coil. Three neuroradiologists evaluated the magnetic resonance images independently, rating the visibility of the nerves in diagnosing hypoplasia or aplasia. Eight ears in seven patients with hypoplasia or aplasia of the cochlear nerve were examined. The average age was 2.7 years (range, 9 months-5 years). Seven ears had accompanying malformations. The inter-rater reliability in diagnosing hypoplasia or aplasia was greater using the high-resolution three-dimensional variable flip-angle turbo spin-echo sequence (fixed-marginal kappa: 0.64) than with the same sequence in lower resolution (fixed-marginal kappa: 0.06). Examining cases of suspected cochlear nerve aplasia using the high-resolution three-dimensional variable flip-angle turbo spin-echo sequence in combination with a surface coil shows significant improvement over standard methods. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

Rapid susceptibility testing and microcolony analysis of Candida spp. cultured and imaged on porous aluminum oxide.

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Colin J Ingham

Full Text Available BACKGROUND: Acquired resistance to antifungal agents now supports the introduction of susceptibility testing for species-drug combinations for which this was previously thought unnecessary. For pathogenic yeasts, conventional phenotypic testing needs at least 24 h. Culture on a porous aluminum oxide (PAO support combined with microscopy offers a route to more rapid results. METHODS: Microcolonies of Candida species grown on PAO were stained with the fluorogenic dyes Fun-1 and Calcofluor White and then imaged by fluorescence microscopy. Images were captured by a charge-coupled device camera and processed by publicly available software. By this method, the growth of yeasts could be detected and quantified within 2 h. Microcolony imaging was then used to assess the susceptibility of the yeasts to amphotericin B, anidulafungin and caspofungin (3.5 h culture, and voriconazole and itraconazole (7 h culture. SIGNIFICANCE: Overall, the results showed good agreement with EUCAST (86.5% agreement; n = 170 and E-test (85.9% agreement; n = 170. The closest agreement to standard tests was found when testing susceptibility to amphotericin B and echinocandins (88.2 to 91.2% and the least good for the triazoles (79.4 to 82.4%. Furthermore, large datasets on population variation could be rapidly obtained. An analysis of microcolonies revealed subtle effects of antimycotics on resistant strains and below the MIC of sensitive strains, particularly an increase in population heterogeneity and cell density-dependent effects of triazoles. Additionally, the method could be adapted to strain identification via germ tube extension. We suggest PAO culture is a rapid and versatile method that may be usefully adapted to clinical mycology and has research applications.

Enhanced learning of natural visual sequences in newborn chicks.

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Wood, Justin N; Prasad, Aditya; Goldman, Jason G; Wood, Samantha M W

2016-07-01

To what extent are newborn brains designed to operate over natural visual input? To address this question, we used a high-throughput controlled-rearing method to examine whether newborn chicks (Gallus gallus) show enhanced learning of natural visual sequences at the onset of vision. We took the same set of images and grouped them into either natural sequences (i.e., sequences showing different viewpoints of the same real-world object) or unnatural sequences (i.e., sequences showing different images of different real-world objects). When raised in virtual worlds containing natural sequences, newborn chicks developed the ability to recognize familiar images of objects. Conversely, when raised in virtual worlds containing unnatural sequences, newborn chicks' object recognition abilities were severely impaired. In fact, the majority of the chicks raised with the unnatural sequences failed to recognize familiar images of objects despite acquiring over 100 h of visual experience with those images. Thus, newborn chicks show enhanced learning of natural visual sequences at the onset of vision. These results indicate that newborn brains are designed to operate over natural visual input.

Generalized min-max bound-based MRI pulse sequence design framework for wide-range T1 relaxometry: A case study on the tissue specific imaging sequence.

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Yang Liu

Full Text Available This paper proposes a new design strategy for optimizing MRI pulse sequences for T1 relaxometry. The design strategy optimizes the pulse sequence parameters to minimize the maximum variance of unbiased T1 estimates over a range of T1 values using the Cramér-Rao bound. In contrast to prior sequences optimized for a single nominal T1 value, the optimized sequence using our bound-based strategy achieves improved precision and accuracy for a broad range of T1 estimates within a clinically feasible scan time. The optimization combines the downhill simplex method with a simulated annealing process. To show the effectiveness of the proposed strategy, we optimize the tissue specific imaging (TSI sequence. Preliminary Monte Carlo simulations demonstrate that the optimized TSI sequence yields improved precision and accuracy over the popular driven-equilibrium single-pulse observation of T1 (DESPOT1 approach for normal brain tissues (estimated T1 700-2000 ms at 3.0T. The relative mean estimation error (MSE for T1 estimation is less than 1.7% using the optimized TSI sequence, as opposed to less than 7.0% using DESPOT1 for normal brain tissues. The optimized TSI sequence achieves good stability by keeping the MSE under 7.0% over larger T1 values corresponding to different lesion tissues and the cerebrospinal fluid (up to 5000 ms. The T1 estimation accuracy using the new pulse sequence also shows improvement, which is more pronounced in low SNR scenarios.

Rapid and Quantitative Assessment of Cancer Treatment Response Using In Vivo Bioluminescence Imaging

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Alnawaz Rehemtulla

2000-01-01

Full Text Available Current assessment of orthotopic tumor models in animals utilizes survival as the primary therapeutic end point. In vivo bioluminescence imaging (BLI is a sensitive imaging modality that is rapid and accessible, and may comprise an ideal tool for evaluating antineoplastic therapies [1 ]. Using human tumor cell lines constitutively expressing luciferase, the kinetics of tumor growth and response to therapy have been assessed in intraperitoneal [2], subcutaneous, and intravascular [3] cancer models. However, use of this approach for evaluating orthotopic tumor models has not been demonstrated. In this report, the ability of BLI to noninvasively quantitate the growth and therapeuticinduced cell kill of orthotopic rat brain tumors derived from 9L gliosarcoma cells genetically engineered to stably express firefly luciferase (9LLuc was investigated. Intracerebral tumor burden was monitored over time by quantitation of photon emission and tumor volume using a cryogenically cooled CCD camera and magnetic resonance imaging (MRI, respectively. There was excellent correlation (r=0.91 between detected photons and tumor volume. A quantitative comparison of tumor cell kill determined from serial MRI volume measurements and BLI photon counts following 1,3-bis(2-chloroethyl-1-nitrosourea (BCNU treatment revealed that both imaging modalities yielded statistically similar cell kill values (P=.951. These results provide direct validation of BLI imaging as a powerful and quantitative tool for the assessment of antineoplastic therapies in living animals.

A bottom-up model of spatial attention predicts human error patterns in rapid scene recognition.

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