Bioluminescence tomography based on the phase approximation model
Cong, W.; Wang, G
2010-01-01
A reconstruction method of bioluminescence sources is proposed based on a phase approximation model. Compared with the diffuse approximation, this phase approximation model more correctly predicts bioluminescence photon propagation in biological tissues, so that bioluminescence tomography can accurately locate and quantify the distribution of bioluminescence sources. The compressive sensing (CS) technique is applied to regularize the inverse source reconstruction to enhance numerical stabilit...
Spectrally resolved bioluminescence tomography using the reciprocity approach
Dehghani, Hamid; Davis, Scott C.; Pogue, Brian W.
2008-01-01
Spectrally resolved bioluminescence optical tomography is an approach to recover images of, for example, Luciferase activity within a volume using multiwavelength emission data from internal bioluminescence sources. The underlying problem of uniqueness associated with nonspectrally resolved intensity-based bioluminescence tomography is demonstrated and it is shown that using a non-negative constraint inverse algorithm, an accurate solution for the source distribution can be calculated from th...
Bioluminescence tomography with Gaussian prior
Gao, Hao; Zhao, Hongkai; Cong, Wenxiang; Wang, Ge
2010-01-01
Parameterizing the bioluminescent source globally in Gaussians provides several advantages over voxel representation in bioluminescence tomography. It is mathematically unique to recover Gaussians [Med. Phys. 31(8), 2289 (2004)] and practically sufficient to approximate various shapes by Gaussians in diffusive medium. The computational burden is significantly reduced since much fewer unknowns are required. Besides, there are physiological evidences that the source can be modeled by Gaussians....
Ultrasound Modulated Bioluminescence Tomography
Bal, Guillaume
2013-01-01
We propose a method to reconstruct the density of a luminescent source in a highly-scattering medium from ultrasound modulated optical measurements. Our approach is based on the solution to a hybrid inverse source problem for the diffusion equation.
Moment searching algorithm for bioluminescence tomography
Ludong Jin; Yan Wu; Jie Tian; Heyu Huang; Xiaochao Qu
2009-01-01
To avoid the ill-posedness in the inverse problem of bioluminescence tomography, a moment searching algorithm fusing the finite element method (FEM) with the moment concept in theoretical mechanics is developed. In the algorithm, the source's information is mapped to the surface photon flux density by FEM, and the source's position is modified with the feedback through the algorithm of barycenter searching, which makes full use of the position information of the photon flux density on surface. The position is modified in every iterative step and will finally converge to the real source's value theoretically.
Multispectral Bioluminescence Tomography: Methodology and Simulation
Ge Wang
2006-02-01
Full Text Available Bioluminescent imaging has proven to be a valuable tool for monitoring physiological and pathological activities at cellular and molecular levels in living small animals. Using biological techniques, target cells can be tagged with reporters encoding several kinds of luciferase enzymes, which generate characteristic photons in a wide spectrum covering the infrared range. Part of the diffused light can reach the body surface of the small animal, be separated into several spectral bands using appropriate filters, and collected by a sensitive CCD camera. Here we present a bioluminescence tomography (BLT method for a bioluminescent source reconstruction from multispectral data measured on the external surface, and demonstrate the advantages of multispectral BLT in a numerical study using a heterogeneous mouse chest phantom. The results show that the multispectral approach significantly improves the accuracy and stability of the BLT reconstruction even if the data are highly noisy.
Automatic Segmentation Framework of Building Anatomical Mouse Model for Bioluminescence Tomography
Abdullah Alali
2013-01-01
Bioluminescence tomography is known as a highly ill-posed inverse problem. To improve the reconstruction performance by introducing anatomical structures as a priori knowledge, an automatic segmentation framework has been proposed in this paper to extract the mouse whole-body organs and tissues, which enables to build up a heterogeneous mouse model for reconstruction of bioluminescence tomography. Finally, an in vivo mouse experiment has been conducted to evaluate this framework by using an X...
A multi-phase level set framework for source reconstruction in bioluminescence tomography
We propose a novel multi-phase level set algorithm for solving the inverse problem of bioluminescence tomography. The distribution of unknown interior source is considered as piecewise constant and represented by using multiple level set functions. The localization of interior bioluminescence source is implemented by tracing the evolution of level set function. An alternate search scheme is incorporated to ensure the global optimal of reconstruction. Both numerical and physical experiments are performed to evaluate the developed level set reconstruction method. Reconstruction results show that the proposed method can stably resolve the interior source of bioluminescence tomography.
Ultrasound-modulated bioluminescence tomography
Bal, Guillaume; Schotland, John C.
2014-03-01
We propose a method to reconstruct the density of a luminescent source in a highly scattering medium from ultrasound-modulated optical measurements. Our approach is based on the solution to a hybrid inverse source problem for the diffusion equation.
Enhanced Landweber algorithm via Bregman iterations for bioluminescence tomography
Xia, Yi; Zhang, Meng
2014-09-01
Bioluminescence tomography (BLT) is an important optical molecular imaging modality aimed at visualizing physiological and pathological processes at cellular and molecular levels. While the forward process of light propagation is described by the diffusion approximation to radiative transfer equation, BLT is the inverse problem to reconstruct the 3D localization and quantification of internal bioluminescent sources distribution. Due to the inherent ill-posedness of the BLT problem, regularization is generally indispensable to obtain more favorable reconstruction. In particular, total variation (TV) regularization is known to be effective for piecewise-constant source distribution which can permit sharp discontinuities and preserve edges. However, total variation regularization generally suffers from the unsatisfactory staircasing effect. In this work, we introduce the Bregman iterative regularization to alleviate this degeneration and enhance the numerical reconstruction of BLT. Based on the existing Landweber method (LM), we put forward the Bregman-LM-TV algorithm for BLT. Numerical experiments are carried out and preliminary simulation results are reported to evaluate the proposed algorithms. It is found that Bregman-LM-TV can significantly outperform the individual Landweber method for BLT when the source distribution is piecewise-constant.
A multithread based new sparse matrix method in bioluminescence tomography
Zhang, Bo; Tian, Jie; Liu, Dan; Sun, Li; Yang, Xin; Han, Dong
2010-03-01
Among many molecular imaging modalities, bioluminescence tomography (BLT) stands out as an effective approach for in vivo imaging because of its noninvasive molecular and cellular level detection ability, high sensitivity and low cost in comparison with other imaging technologies. However, there exists the case that large scale problem with large number of points and elements in the structure of mesh standing for the small animal or phantom. And the large scale problem's system matrix generated by the diffuse approximation (DA) model using finite element method (FEM) is large. So there wouldn't be enough random access memory (RAM) for the program and the related inverse problem couldn't be solved. Considering the sparse property of the BLT system matrix, we've developed a new sparse matrix (ZSM) to overcome the problem. And the related algorithms have all been speeded up by multi-thread technologies. Then the inverse problem is solved by Tikhonov regularization method in adaptive finite element (AFE) framework. Finally, the performance of this method is tested on a heterogeneous phantom and the boundary data is obtained through Monte Carlo simulation. During the process of solving the forward model, the ZSM can save more processing time and memory space than the usual way, such as those not using sparse matrix and those using Triples or Cross Linked sparse matrix. Numerical experiments have shown when more CPU cores are used, the processing speed is increased. By incorporating ZSM, BLT can be applied to large scale problems with large system matrix.
Mathematical Study and Numerical Simulation of Multispectral Bioluminescence Tomography
Weimin Han; Wenxiang Cong; Ge Wang
2006-01-01
Multispectral bioluminescence tomography (BLT) attracts increasingly more attention in the area of optical molecular imaging. In this paper, we analyze the properties of the solutions to the regularized and discretized multispectral BLT problems. First, we show the solution existence, uniqueness, and its continuous dependence on the data. Then, we introduce stable numerical schemes and derive error estimates for numerical solutions. We report some numerical results to illust...
Experimental Study on Bioluminescence Tomography with Multimodality Fusion
Lv, Yujie; Tian, Jie; Cong, Wenxiang; Wang, Ge
2007-01-01
To verify the influence of a priori information on the nonuniqueness problem of bioluminescence tomography (BLT), the multimodality imaging fusion based BLT experiment is performed by multiview noncontact detection mode, which incorporates the anatomical information obtained by the microCT scanner and the background optical properties based on diffuse reflectance measurements. In the reconstruction procedure, the utilization of adaptive finite element methods (FEMs) and a priori permissible s...
In Vivo Mouse Bioluminescence Tomography with Radionuclide-Based Imaging Validation
Lu, Yujie; Machado, Hidevaldo B.; Bao, Qinan; Stout, David; Herschman, Harvey; Chatziioannou, Arion F.
2010-01-01
Introduction Bioluminescence imaging, especially planar bioluminescence imaging, has been extensively applied in in vivo preclinical biological research. Bioluminescence tomography (BLT) has the potential to provide more accurate imaging information due to its 3D reconstruction compared with its planar counterpart. Methods In this work, we introduce a positron emission tomography (PET) radionuclide imaging-based strategy to validate the BLT results. X-ray computed tomography, PET, spectrally ...
Even though bioluminescence tomography (BLT) exhibits significant potential and wide applications in macroscopic imaging of small animals in vivo, the inverse reconstruction is still a tough problem that has plagued researchers in a related area. The ill-posedness of inverse reconstruction arises from insufficient measurements and modeling errors, so that the inverse reconstruction cannot be solved directly. In this study, an l1/2 regularization based numerical method was developed for effective reconstruction of BLT. In the method, the inverse reconstruction of BLT was constrained into an l1/2 regularization problem, and then the weighted interior-point algorithm (WIPA) was applied to solve the problem through transforming it into obtaining the solution of a series of l1 regularizers. The feasibility and effectiveness of the proposed method were demonstrated with numerical simulations on a digital mouse. Stability verification experiments further illustrated the robustness of the proposed method for different levels of Gaussian noise
Chen, Xueli; Yang, Defu; Zhang, Qitan; Liang, Jimin
2014-05-01
Even though bioluminescence tomography (BLT) exhibits significant potential and wide applications in macroscopic imaging of small animals in vivo, the inverse reconstruction is still a tough problem that has plagued researchers in a related area. The ill-posedness of inverse reconstruction arises from insufficient measurements and modeling errors, so that the inverse reconstruction cannot be solved directly. In this study, an l1/2 regularization based numerical method was developed for effective reconstruction of BLT. In the method, the inverse reconstruction of BLT was constrained into an l1/2 regularization problem, and then the weighted interior-point algorithm (WIPA) was applied to solve the problem through transforming it into obtaining the solution of a series of l1 regularizers. The feasibility and effectiveness of the proposed method were demonstrated with numerical simulations on a digital mouse. Stability verification experiments further illustrated the robustness of the proposed method for different levels of Gaussian noise.
In vivo bioluminescence tomography based on multi-view projection and 3D surface reconstruction
Zhang, Shuang; Wang, Kun; Leng, Chengcai; Deng, Kexin; Hu, Yifang; Tian, Jie
2015-03-01
Bioluminescence tomography (BLT) is a powerful optical molecular imaging modality, which enables non-invasive realtime in vivo imaging as well as 3D quantitative analysis in preclinical studies. In order to solve the inverse problem and reconstruct inner light sources accurately, the prior structural information is commonly necessary and obtained from computed tomography or magnetic resonance imaging. This strategy requires expensive hybrid imaging system, complicated operation protocol and possible involvement of ionizing radiation. The overall robustness highly depends on the fusion accuracy between the optical and structural information. In this study we present a pure optical bioluminescence tomographic system (POBTS) and a novel BLT method based on multi-view projection acquisition and 3D surface reconstruction. The POBTS acquired a sparse set of white light surface images and bioluminescent images of a mouse. Then the white light images were applied to an approximate surface model to generate a high quality textured 3D surface reconstruction of the mouse. After that we integrated multi-view luminescent images based on the previous reconstruction, and applied an algorithm to calibrate and quantify the surface luminescent flux in 3D.Finally, the internal bioluminescence source reconstruction was achieved with this prior information. A BALB/C mouse with breast tumor of 4T1-fLuc cells mouse model were used to evaluate the performance of the new system and technique. Compared with the conventional hybrid optical-CT approach using the same inverse reconstruction method, the reconstruction accuracy of this technique was improved. The distance error between the actual and reconstructed internal source was decreased by 0.184 mm.
Experimental Study on Bioluminescence Tomography with Multimodality Fusion
Yujie Lv
2007-01-01
Full Text Available To verify the influence of a priori information on the nonuniqueness problem of bioluminescence tomography (BLT, the multimodality imaging fusion based BLT experiment is performed by multiview noncontact detection mode, which incorporates the anatomical information obtained by the microCT scanner and the background optical properties based on diffuse reflectance measurements. In the reconstruction procedure, the utilization of adaptive finite element methods (FEMs and a priori permissible source region refines the reconstructed results and improves numerical robustness and efficiency. The comparison between the absence and employment of a priori information shows that multimodality imaging fusion is essential to quantitative BLT reconstruction.
BIOLUMINESCENCE TOMOGRAPHY: BIOMEDICAL BACKGROUND, MATHEMATICAL THEORY, AND NUMERICAL APPROXIMATION
Weimin Han; Ce Wang
2008-01-01
Over the last couple of years molecular imaging has been rapidly developed to study physiological and pathological processes in vivo at the cellular and molecular levels. Among molecular imaging modalities, optical imaging stands out for its unique advantages, especially performance and cost-effectiveness. Bioluminescence tomography (BLT) is an emerging optical imaging mode with promising biomedical advantages. In this survey paper, we explain the biomedical significance of BLT, summarize theoretical results on the analysis and numerical solution of a diffusion based BLT model, and comment on a few extensions for the study of BLT.
An adaptive regularization parameter choice strategy for multispectral bioluminescence tomography
Purpose: Bioluminescence tomography (BLT) provides an effective tool for monitoring physiological and pathological activities in vivo. However, the measured data in bioluminescence imaging are corrupted by noise. Therefore, regularization methods are commonly used to find a regularized solution. Nevertheless, for the quality of the reconstructed bioluminescent source obtained by regularization methods, the choice of the regularization parameters is crucial. To date, the selection of regularization parameters remains challenging. With regards to the above problems, the authors proposed a BLT reconstruction algorithm with an adaptive parameter choice rule. Methods: The proposed reconstruction algorithm uses a diffusion equation for modeling the bioluminescent photon transport. The diffusion equation is solved with a finite element method. Computed tomography (CT) images provide anatomical information regarding the geometry of the small animal and its internal organs. To reduce the ill-posedness of BLT, spectral information and the optimal permissible source region are employed. Then, the relationship between the unknown source distribution and multiview and multispectral boundary measurements is established based on the finite element method and the optimal permissible source region. Since the measured data are noisy, the BLT reconstruction is formulated as l2 data fidelity and a general regularization term. When choosing the regularization parameters for BLT, an efficient model function approach is proposed, which does not require knowledge of the noise level. This approach only requests the computation of the residual and regularized solution norm. With this knowledge, we construct the model function to approximate the objective function, and the regularization parameter is updated iteratively. Results: First, the micro-CT based mouse phantom was used for simulation verification. Simulation experiments were used to illustrate why multispectral data were used rather
An adaptive regularization parameter choice strategy for multispectral bioluminescence tomography
Feng Jinchao; Qin Chenghu; Jia Kebin; Han Dong; Liu Kai; Zhu Shouping; Yang Xin; Tian Jie [Medical Image Processing Group, Institute of Automation, Chinese Academy of Sciences, P. O. Box 2728, Beijing 100190 (China); College of Electronic Information and Control Engineering, Beijing University of Technology, Beijing 100124 (China); Medical Image Processing Group, Institute of Automation, Chinese Academy of Sciences, P. O. Box 2728, Beijing 100190 (China); Medical Image Processing Group, Institute of Automation, Chinese Academy of Sciences, P. O. Box 2728, Beijing 100190 (China) and School of Life Sciences and Technology, Xidian University, Xi' an 710071 (China)
2011-11-15
Purpose: Bioluminescence tomography (BLT) provides an effective tool for monitoring physiological and pathological activities in vivo. However, the measured data in bioluminescence imaging are corrupted by noise. Therefore, regularization methods are commonly used to find a regularized solution. Nevertheless, for the quality of the reconstructed bioluminescent source obtained by regularization methods, the choice of the regularization parameters is crucial. To date, the selection of regularization parameters remains challenging. With regards to the above problems, the authors proposed a BLT reconstruction algorithm with an adaptive parameter choice rule. Methods: The proposed reconstruction algorithm uses a diffusion equation for modeling the bioluminescent photon transport. The diffusion equation is solved with a finite element method. Computed tomography (CT) images provide anatomical information regarding the geometry of the small animal and its internal organs. To reduce the ill-posedness of BLT, spectral information and the optimal permissible source region are employed. Then, the relationship between the unknown source distribution and multiview and multispectral boundary measurements is established based on the finite element method and the optimal permissible source region. Since the measured data are noisy, the BLT reconstruction is formulated as l{sub 2} data fidelity and a general regularization term. When choosing the regularization parameters for BLT, an efficient model function approach is proposed, which does not require knowledge of the noise level. This approach only requests the computation of the residual and regularized solution norm. With this knowledge, we construct the model function to approximate the objective function, and the regularization parameter is updated iteratively. Results: First, the micro-CT based mouse phantom was used for simulation verification. Simulation experiments were used to illustrate why multispectral data were used
Jones, M. Gail
1993-01-01
Describes bioluminescence and the chemistry of how it occurs. Presents information for conducting the following classroom activities: (1) firefly mimic; (2) modeling deep-sea fish; (3) sea fireflies; and (4) the chemistry of light. (PR)
Emerging fluorescence and bioluminescence tomography approaches have several common, yet several distinct features from established emission tomographies of PET and SPECT. Although both nuclear and optical imaging modalities involve counting of photons, nuclear imaging techniques collect the emitted high energy (100–511 keV) photons after radioactive decay of radionuclides while optical techniques count low-energy (1.5–4.1 eV) photons that are scattered and absorbed by tissues requiring models of light transport for quantitative image reconstruction. Fluorescence imaging has been recently translated into clinic demonstrating high sensitivity, modest tissue penetration depth, and fast, millisecond image acquisition times. As a consequence, the promise of quantitative optical tomography as a complement of small animal PET and SPECT remains high. In this review, we summarize the different instrumentation, methodological approaches and schema for inverse image reconstructions for optical tomography, including luminescence and fluorescence modalities, and comment on limitations and key technological advances needed for further discovery research and translation. (topical review)
Darne, Chinmay; Lu, Yujie; Sevick-Muraca, Eva M.
2014-01-01
Emerging fluorescence and bioluminescence tomography approaches have several common, yet several distinct features from established emission tomographies of PET and SPECT. Although both nuclear and optical imaging modalities involve counting of photons, nuclear imaging techniques collect the emitted high energy (100-511 keV) photons after radioactive decay of radionuclides while optical techniques count low-energy (1.5-4.1 eV) photons that are scattered and absorbed by tissues requiring models of light transport for quantitative image reconstruction. Fluorescence imaging has been recently translated into clinic demonstrating high sensitivity, modest tissue penetration depth, and fast, millisecond image acquisition times. As a consequence, the promise of quantitative optical tomography as a complement of small animal PET and SPECT remains high. In this review, we summarize the different instrumentation, methodological approaches and schema for inverse image reconstructions for optical tomography, including luminescence and fluorescence modalities, and comment on limitations and key technological advances needed for further discovery research and translation.
He, Xiaowei; Yu, Jingjing; Geng, Guohua; Guo, Hongbo
2013-10-01
As an important optical molecular imaging technique, bioluminescence tomography (BLT) offers an inexpensive and sensitive means for non-invasively imaging a variety of physiological and pathological activities at cellular and molecular levels in living small animals. The key problem of BLT is to recover the distribution of the internal bioluminescence sources from limited measurements on the surface. Considering the sparsity of the light source distribution, we directly formulate the inverse problem of BLT into an l0-norm minimization model and present a smoothed l0-norm (SL0) based reconstruction algorithm. By approximating the discontinuous l0 norm with a suitable continuous function, the SL0 norm method solves the problem of intractable computational load of the minimal l0 search as well as high sensitivity of l0-norm to noise. Numerical experiments on a mouse atlas demonstrate that the proposed SL0 norm based reconstruction method can obtain whole domain reconstruction without any a priori knowledge of the source permissible region, yielding almost the same reconstruction results to those of l1 norm methods.
Chen, Xueli, E-mail: xlchen@xidian.edu.cn, E-mail: jimleung@mail.xidian.edu.cn; Yang, Defu; Zhang, Qitan; Liang, Jimin, E-mail: xlchen@xidian.edu.cn, E-mail: jimleung@mail.xidian.edu.cn [School of Life Science and Technology, Xidian University, Xi' an 710071 (China); Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education (China)
2014-05-14
Even though bioluminescence tomography (BLT) exhibits significant potential and wide applications in macroscopic imaging of small animals in vivo, the inverse reconstruction is still a tough problem that has plagued researchers in a related area. The ill-posedness of inverse reconstruction arises from insufficient measurements and modeling errors, so that the inverse reconstruction cannot be solved directly. In this study, an l{sub 1/2} regularization based numerical method was developed for effective reconstruction of BLT. In the method, the inverse reconstruction of BLT was constrained into an l{sub 1/2} regularization problem, and then the weighted interior-point algorithm (WIPA) was applied to solve the problem through transforming it into obtaining the solution of a series of l{sub 1} regularizers. The feasibility and effectiveness of the proposed method were demonstrated with numerical simulations on a digital mouse. Stability verification experiments further illustrated the robustness of the proposed method for different levels of Gaussian noise.
Klose, Alexander D.; Beattie, Bradley J.; Dehghani, Hamid; Vider, Lena; Le, Carl; Ponomarev, Vladimir; Blasberg, Ronald
2009-01-01
Purpose: Bioluminescence imaging is a research tool for studying gene expression levels in small animal models of human disease. Bioluminescence light, however, is strongly scattered in biological tissue and no direct image of the light-emitting reporter probe’s location can be obtained. Therefore, the authors have developed a linear image reconstruction method for bioluminescence tomography (BLT) that recovers the three-dimensional spatial bioluminescent source distribution in small animals.
A novel reconstruction algorithm for bioluminescent tomography based on Bayesian compressive sensing
Wang, Yaqi; Feng, Jinchao; Jia, Kebin; Sun, Zhonghua; Wei, Huijun
2016-03-01
Bioluminescence tomography (BLT) is becoming a promising tool because it can resolve the biodistribution of bioluminescent reporters associated with cellular and subcellular function through several millimeters with to centimeters of tissues in vivo. However, BLT reconstruction is an ill-posed problem. By incorporating sparse a priori information about bioluminescent source, enhanced image quality is obtained for sparsity based reconstruction algorithm. Therefore, sparsity based BLT reconstruction algorithm has a great potential. Here, we proposed a novel reconstruction method based on Bayesian compressive sensing and investigated its feasibility and effectiveness with a heterogeneous phantom. The results demonstrate the potential and merits of the proposed algorithm.
Fast iterative image reconstruction methods for fully 3D multispectral bioluminescence tomography
We investigate fast iterative image reconstruction methods for fully 3D multispectral bioluminescence tomography for applications in small animal imaging. Our forward model uses a diffusion approximation for optically inhomogeneous tissue, which we solve using a finite element method (FEM). We examine two approaches to incorporating the forward model into the solution of the inverse problem. In a conventional direct calculation approach one computes the full forward model by repeated solution of the FEM problem, once for each potential source location. We describe an alternative on-the-fly approach where one does not explicitly solve for the full forward model. Instead, the solution to the forward problem is included implicitly in the formulation of the inverse problem, and the FEM problem is solved at each iteration for the current image estimate. We evaluate the convergence speeds of several representative iterative algorithms. We compare the computation cost of those two approaches, concluding that the on-the-fly approach can lead to substantial reductions in total cost when combined with a rapidly converging iterative algorithm
Design and implementation of an optical simulation environment for bioluminescent tomography studies
LI Hui; TIAN Jie; LUO Jie; L(U) Yujie; CONG Wenxiang; WANG Ge
2007-01-01
As a challenging task for bioluminescent tomography simulation, a virtual optical environment is needed to solve the forward problem accurately, that is, to achieve a high precision for bioluminescent signal synthesis on the external body surface of a small animal. The molecular optical simulation environment named MOSE is implemented using the C + + programming language and the OpenGL techniques, including a user-friendly interface with interactive tools facilitating users' operations. The accuracy of the virtual optical environment is verified by error analysis of mesh simplification and comparison between MOSE results and experimental data. This virtual optical environment is accurate, flexible and efficient to simulate the photon propagation in complicated tissues, which has a great potential to become a software platform for bioluminescent tomography studies and other molecular imaging applications.
Bioluminescence imaging has been extensively applied to in vivo small animal imaging. Quantitative three-dimensional bioluminescent source information obtained by using bioluminescence tomography can directly and much more accurately reflect biological changes as opposed to planar bioluminescence imaging. Preliminary simulated and experimental reconstruction results demonstrate the feasibility and promise of bioluminescence tomography. However, the use of multiple approximations, particularly the diffusion approximation theory, affects the quality of in vivo small animal-based image reconstructions. In the development of new reconstruction algorithms, high-order approximation models of the radiative transfer equation and spectrally resolved data introduce new challenges to the reconstruction algorithm and speed. In this paper, an SP3-based (the third-order simplified spherical harmonics approximation) spectrally resolved reconstruction algorithm is proposed. The simple linear relationship between the unknown source distribution and the spectrally resolved data is established in this algorithm. A parallel version of this algorithm is realized, making BLT reconstruction feasible for the whole body of small animals especially for fine spatial domain discretization. In simulation validations, the proposed algorithm shows improved reconstruction quality compared with diffusion approximation-based methods when high absorption, superficial sources and detection modes are considered. In addition, comparisons between fine and coarse mesh-based BLT reconstructions show the effects of numerical errors in reconstruction image quality. Finally, BLT reconstructions using in vivo mouse experiments further demonstrate the potential and effectiveness of the SP3-based reconstruction algorithm.
Hyperspectral and multispectral bioluminescence optical tomography for small animal imaging
For bioluminescence imaging studies in small animals, it is important to be able to accurately localize the three-dimensional (3D) distribution of the underlying bioluminescent source. The spectrum of light produced by the source that escapes the subject varies with the depth of the emission source because of the wavelength-dependence of the optical properties of tissue. Consequently, multispectral or hyperspectral data acquisition should help in the 3D localization of deep sources. In this paper, we describe a framework for fully 3D bioluminescence tomographic image acquisition and reconstruction that exploits spectral information. We describe regularized tomographic reconstruction techniques that use semi-infinite slab or FEM-based diffusion approximations of photon transport through turbid media. Singular value decomposition analysis was used for data dimensionality reduction and to illustrate the advantage of using hyperspectral rather than achromatic data. Simulation studies in an atlas-mouse geometry indicated that sub-millimeter resolution may be attainable given accurate knowledge of the optical properties of the animal. A fixed arrangement of mirrors and a single CCD camera were used for simultaneous acquisition of multispectral imaging data over most of the surface of the animal. Phantom studies conducted using this system demonstrated our ability to accurately localize deep point-like sources and show that a resolution of 1.5 to 2.2 mm for depths up to 6 mm can be achieved. We also include an in vivo study of a mouse with a brain tumour expressing firefly luciferase. Co-registration of the reconstructed 3D bioluminescent image with magnetic resonance images indicated good anatomical localization of the tumour
Ge Wang
2006-01-01
Full Text Available We describe the system design of the first bioluminescence tomography (BLT system for parallel acquisition of multiple bioluminescent views around a mouse in a number of spectral channels simultaneously. The primary component of this BLT system is a novel mirror module and a unique mouse holder. The mirror module consists of a mounting plate and four mirrors with stages. These mirror stages are right triangular blocks symmetrically arranged and attached to the mounting plate such that the hypotenuse surfaces of the triangular blocks all make 45∘ to the plate surface. The cylindrical/polygonal mouse holder has semitransparent rainbow bands on its side surface for the acquisition of spectrally resolved data. Numerical studies and experiments are performed to demonstrate the feasibility of this system. It is shown that bioluminescent signals collected using our system can produce a similar BLT reconstruction quality while reducing the data acquisition time, as compared to the sequential data acquisition mode.
A reconstruction algorithm for diffuse optical tomography based on diffusion theory and finite element method is described. The algorithm reconstructs the optical properties in a permissible domain or region-of-interest to reduce the number of unknowns. The algorithm can be used to reconstruct optical properties for a segmented object (where a CT-scan or MRI is available) or a non-segmented object. For the latter, an adaptive segmentation algorithm merges contiguous regions with similar optical properties thereby reducing the number of unknowns. In calculating the Jacobian matrix the algorithm uses an efficient direct method so the required time is comparable to that needed for a single forward calculation. The reconstructed optical properties using segmented, non-segmented, and adaptively segmented 3D mouse anatomy (MOBY) are used to perform bioluminescence tomography (BLT) for two simulated internal sources. The BLT results suggest that the accuracy of reconstruction of total source power obtained without the segmentation provided by an auxiliary imaging method such as x-ray CT is comparable to that obtained when using perfect segmentation. (paper)
Naser, Mohamed A.; Patterson, Michael S.; Wong, John W.
2014-04-01
A reconstruction algorithm for diffuse optical tomography based on diffusion theory and finite element method is described. The algorithm reconstructs the optical properties in a permissible domain or region-of-interest to reduce the number of unknowns. The algorithm can be used to reconstruct optical properties for a segmented object (where a CT-scan or MRI is available) or a non-segmented object. For the latter, an adaptive segmentation algorithm merges contiguous regions with similar optical properties thereby reducing the number of unknowns. In calculating the Jacobian matrix the algorithm uses an efficient direct method so the required time is comparable to that needed for a single forward calculation. The reconstructed optical properties using segmented, non-segmented, and adaptively segmented 3D mouse anatomy (MOBY) are used to perform bioluminescence tomography (BLT) for two simulated internal sources. The BLT results suggest that the accuracy of reconstruction of total source power obtained without the segmentation provided by an auxiliary imaging method such as x-ray CT is comparable to that obtained when using perfect segmentation.
Direct and inverse problems of infrared tomography
Sizikov, Valery S.; Evseev, Vadim; Fateev, Alexander;
2016-01-01
The problems of infrared tomography-direct (the modeling of measured functions) and inverse (the reconstruction of gaseous medium parameters)-are considered with a laboratory burner flame as an example of an application. The two measurement modes are used: active (ON) with an external IR source and...
As a molecular imaging technique, bioluminescence tomography (BLT) with its highly sensitive detection and facile operation can significantly reveal molecular and cellular information in vivo at the whole-body small animal level. However, because of complex photon transportation in biological tissue and boundary detection data with high noise, bioluminescent sources in deeper positions generally cannot be localized. In our previous work, we used achromatic or monochromatic measurements and an a priori permissible source region strategy to develop a multilevel adaptive finite-element algorithm. In this paper, we propose a spectrally solved tomographic algorithm with a posteriori permissible source region selection. Multispectral measurements, and anatomical and optical information first deal with the nonuniqueness of BLT and constrain the possible solution of source reconstruction. The use of adaptive mesh refinement and permissible source region based on a posteriori measures not only avoids the dimension disaster arising from the multispectral measured data but also reduces the ill-posedness of BLT and therefore improves the reconstruction quality. Reconsideration of the optimization method and related modifications further enhance reconstruction robustness and efficiency. We also incorporate into the method some improvements for reducing computational burdens. Finally, using a whole-body virtual mouse phantom, we demonstrate the capability of the proposed BLT algorithm to reconstruct accurately bioluminescent sources in deeper positions. In terms of optical property errors and two sources of discernment in deeper positions, this BLT algorithm represents the unique predominance for BLT reconstruction
Chen, Xueli; Liang, Jimin; Hu, Hao; Qu, Xiaochao; Yang, Defu; Chen, Duofang; Zhu, Shouping; Tian, Jie
2012-03-01
Gastric cancer is the second cause of cancer-related death in the world, and it remains difficult to cure because it has been in late-stage once that is found. Early gastric cancer detection becomes an effective approach to decrease the gastric cancer mortality. Bioluminescence tomography (BLT) has been applied to detect early liver cancer and prostate cancer metastasis. However, the gastric cancer commonly originates from the gastric mucosa and grows outwards. The bioluminescent light will pass through a non-scattering region constructed by gastric pouch when it transports in tissues. Thus, the current BLT reconstruction algorithms based on the approximation model of radiative transfer equation are not optimal to handle this problem. To address the gastric cancer specific problem, this paper presents a novel reconstruction algorithm that uses a hybrid light transport model to describe the bioluminescent light propagation in tissues. The radiosity theory integrated with the diffusion equation to form the hybrid light transport model is utilized to describe light propagation in the non-scattering region. After the finite element discretization, the hybrid light transport model is converted into a minimization problem which fuses an l1 norm based regularization term to reveal the sparsity of bioluminescent source distribution. The performance of the reconstruction algorithm is first demonstrated with a digital mouse based simulation with the reconstruction error less than 1mm. An in situ gastric cancer-bearing nude mouse based experiment is then conducted. The primary result reveals the ability of the novel BLT reconstruction algorithm in early gastric cancer detection.
Ren, Shenghan; Hu, Haihong; Li, Gen; Cao, Xu; Zhu, Shouping; Chen, Xueli; Liang, Jimin
2016-01-01
Bioluminescence tomography (BLT) has been a valuable optical molecular imaging technique to non-invasively depict the cellular and molecular processes in living animals with high sensitivity and specificity. Due to the inherent ill-posedness of BLT, a priori information of anatomical structure is usually incorporated into the reconstruction. The structural information is usually provided by computed tomography (CT) or magnetic resonance imaging (MRI). In order to obtain better quantitative results, BLT reconstruction with heterogeneous tissues needs to segment the internal organs and discretize them into meshes with the finite element method (FEM). It is time-consuming and difficult to handle the segmentation and discretization problems. In this paper, we present a fast reconstruction method for BLT based on multi-atlas registration and adaptive voxel discretization to relieve the complicated data processing procedure involved in the hybrid BLT/CT system. A multi-atlas registration method is first adopted to estimate the internal organ distribution of the imaged animal. Then, the animal volume is adaptively discretized into hexahedral voxels, which are fed into FEM for the following BLT reconstruction. The proposed method is validated in both numerical simulation and an in vivo study. The results demonstrate that the proposed method can reconstruct the bioluminescence source efficiently with satisfactory accuracy.
Ren, Shenghan; Hu, Haihong; Li, Gen; Cao, Xu; Zhu, Shouping; Chen, Xueli; Liang, Jimin
2016-04-01
Bioluminescence tomography (BLT) has been a valuable optical molecular imaging technique to non-invasively depict the cellular and molecular processes in living animals with high sensitivity and specificity. Due to the inherent ill-posedness of BLT, a priori information of anatomical structure is usually incorporated into the reconstruction. The structural information is usually provided by computed tomography (CT) or magnetic resonance imaging (MRI). In order to obtain better quantitative results, BLT reconstruction with heterogeneous tissues needs to segment the internal organs and discretize them into meshes with the finite element method (FEM). It is time-consuming and difficult to handle the segmentation and discretization problems. In this paper, we present a fast reconstruction method for BLT based on multi-atlas registration and adaptive voxel discretization to relieve the complicated data processing procedure involved in the hybrid BLT/CT system. A multi-atlas registration method is first adopted to estimate the internal organ distribution of the imaged animal. Then, the animal volume is adaptively discretized into hexahedral voxels, which are fed into FEM for the following BLT reconstruction. The proposed method is validated in both numerical simulation and an in vivo study. The results demonstrate that the proposed method can reconstruct the bioluminescence source efficiently with satisfactory accuracy. PMID:27446674
Improved AFEM algorithm for bioluminescence tomography based on dual-mesh alternation strategy
Wei Li; Heng Zhao; Xiaochao Qu; Yanbin Hou; Xueli Chen; Duofang Chen; Xiaowei He; Qitan Zhang; Jimin Liang
2012-01-01
Adaptive finite element method (AFEM) is broadly adopted to recover the internal source in biological tissues.In this letter,a novel dual-mesh alternation strategy (dual-mesh AFEM) is developed for bioluminescence tomography.By comprehensively considering the error estimation of the finite element method solution on each mesh,two different adaptive strategies based on the error indicator of the reconstructed source and the photon flux density are used alternately in the process.Combined with the constantly adjusted permissible region in the adaptive process,the new algorithm can achieve a more accurate source location compared with the AFEM in the previous experiments.%Adaptive finite element method (AFEM) is broadly adopted to recover the internal source in biological tissues. In this letter, a novel dual-mesh alternation strategy (dual-mesh AFEM) is developed for biolumi-nescence tomography. By comprehensively considering the error estimation of the finite element method solution on each mesh, two different adaptive strategies based on the error indicator of the reconstructed source and the photon flux density are used alternately in the process. Combined with the constantly adjusted permissible region in the adaptive process, the new algorithm can achieve a more accurate source location compared with the AFEM in the previous experiments.
Jingjing Yu
2013-01-01
Full Text Available Quantitative reconstruction of bioluminescent sources from boundary measurements is a challenging ill-posed inverse problem owing to the high degree of absorption and scattering of light through tissue. We present a hybrid multilevel reconstruction scheme by combining the ability of sparse regularization with the advantage of adaptive finite element method. In view of the characteristics of different discretization levels, two different inversion algorithms are employed on the initial coarse mesh and the succeeding ones to strike a balance between stability and efficiency. Numerical experiment results with a digital mouse model demonstrate that the proposed scheme can accurately localize and quantify source distribution while maintaining reconstruction stability and computational economy. The effectiveness of this hybrid reconstruction scheme is further confirmed with in vivo experiments.
Accounting for filter bandwidth improves the quantitative accuracy of bioluminescence tomography
Taylor, Shelley L.; Mason, Suzannah K. G.; Glinton, Sophie L.; Cobbold, Mark; Dehghani, Hamid
2015-09-01
Bioluminescence imaging is a noninvasive technique whereby surface weighted images of luminescent probes within animals are used to characterize cell count and function. Traditionally, data are collected over the entire emission spectrum of the source using no filters and are used to evaluate cell count/function over the entire spectrum. Alternatively, multispectral data over several wavelengths can be incorporated to perform tomographic reconstruction of source location and intensity. However, bandpass filters used for multispectral data acquisition have a specific bandwidth, which is ignored in the reconstruction. In this work, ignoring the bandwidth is shown to introduce a dependence of the recovered source intensity on the bandwidth of the filters. A method of accounting for the bandwidth of filters used during multispectral data acquisition is presented and its efficacy in increasing the quantitative accuracy of bioluminescence tomography is demonstrated through simulation and experiment. It is demonstrated that while using filters with a large bandwidth can dramatically decrease the data acquisition time, if not accounted for, errors of up to 200% in quantitative accuracy are introduced in two-dimensional planar imaging, even after normalization. For tomographic imaging, the use of this method to account for filter bandwidth dramatically improves the quantitative accuracy.
Zhang, Bin; Iordachita, Iulian; Wong, John W.; Wang, Ken Kang-Hsin
2016-03-01
Cone beam computed tomography (CBCT) is limited in guiding irradiation for soft tissue targets. As a complementary imaging modality, bioluminescence tomography (BLT) provides strong soft tissue contrast. We developed a dual-use BLT system which consists of an optical assembly, a mobile cart and an independent mouse bed. The system is motorized which can easily dock onto an independent mouse bed operating as a standalone system for longitudinal bioluminescence imaging (BLI)/BLT studies and also dock onto the SARRP for on-line radiation guidance. Our initial tests for the system demonstrate that (i) the imaging depth is 28 mm, (ii) the optical background is sufficiently low and uniform, (iii) the non-uniform response of the optical imaging can be corrected by the flat field correction, and (iv) the imaging acquisition speed was improved by an average of 3.7 times faster than our previous systems. We also presented a geometry calibration procedure to map the planar BLIs acquired at multi-projections onto the surface of the CBCT image. The CBCT is required to generate the mesh for BLT reconstruction and used for treatment planning and radiation delivery. Feasibility study of the geometry calibration was performed on a manual-docking prototype. The mean and maximum mapping accuracy is 0.3 and 0.6 mm. The performance of the proposed motorized dual-use system is expected to be superior to that of the manual-docking prototype because of the mechanism stability. We anticipate the dual-use system as a highly efficient and cost-effective platform to facilitate optical imaging for preclinical radiation research.
Direct and inverse problems of infrared tomography.
Sizikov, Valery S; Evseev, Vadim; Fateev, Alexander; Clausen, Sønnik
2016-01-01
The problems of infrared tomography-direct (the modeling of measured functions) and inverse (the reconstruction of gaseous medium parameters)-are considered with a laboratory burner flame as an example of an application. The two measurement modes are used: active (ON) with an external IR source and passive (OFF) without one. Received light intensities on detectors are modeled in the direct problem or measured in the experiment whereas integral equations with respect to the absorption coefficient and Planck function (which yields the temperature profile of the medium) are solved in the inverse problem with (1) modeled and (2) measured received intensities as the input data. An axisymmetric flame and parallel scanning scheme of measurements considered in this work yield singular integral equations that are solved numerically using the generalized quadrature method, spline smoothing, and Tikhonov regularization. A software package in MATLAB has been developed. Two numerical examples-with modeled and real input data-were solved. The proposed methodology avoids the necessity of elaborate determination of the absorption coefficient by direct (point) measurements or calculation using spectroscopic databases (e.g., HITRAN/HITEMP). PMID:26835642
Iterative Reconstruction Methods for Hybrid Inverse Problems in Impedance Tomography
Hoffmann, Kristoffer; Knudsen, Kim
2014-01-01
For a general formulation of hybrid inverse problems in impedance tomography the Picard and Newton iterative schemes are adapted and four iterative reconstruction algorithms are developed. The general problem formulation includes several existing hybrid imaging modalities such as current density...
To provide an ideal solution for a specific problem of gastric cancer detection in which low-scattering regions simultaneously existed with both the non- and high-scattering regions, a novel hybrid radiosity-SP3 equation based reconstruction algorithm for bioluminescence tomography was proposed in this paper. In the algorithm, the third-order simplified spherical harmonics approximation (SP3) was combined with the radiosity equation to describe the bioluminescent light propagation in tissues, which provided acceptable accuracy for the turbid medium with both low- and non-scattering regions. The performance of the algorithm was evaluated with digital mouse based simulations and a gastric cancer-bearing mouse based in situ experiment. Primary results demonstrated the feasibility and superiority of the proposed algorithm for the turbid medium with low- and non-scattering regions
Chen, Xueli; Zhang, Qitan; Yang, Defu; Liang, Jimin
2014-01-01
To provide an ideal solution for a specific problem of gastric cancer detection in which low-scattering regions simultaneously existed with both the non- and high-scattering regions, a novel hybrid radiosity-SP3 equation based reconstruction algorithm for bioluminescence tomography was proposed in this paper. In the algorithm, the third-order simplified spherical harmonics approximation (SP3) was combined with the radiosity equation to describe the bioluminescent light propagation in tissues, which provided acceptable accuracy for the turbid medium with both low- and non-scattering regions. The performance of the algorithm was evaluated with digital mouse based simulations and a gastric cancer-bearing mouse based in situ experiment. Primary results demonstrated the feasibility and superiority of the proposed algorithm for the turbid medium with low- and non-scattering regions.
Supercomputer technologies in inverse problems of ultrasound tomography
This study focuses on the development of efficient methods for solving inverse problems of ultrasound tomography as coefficient inverse problems for the wave equation. The inverse problem consists in finding the unknown wave propagation velocity as a function of coordinates in three-dimensional space. Efficient iterative methods are proposed for solving the inverse problem based on a direct computation of the residual functional. One of the most promising directions of ultrasound tomography is the development of ultrasound tomographs for medical research, and primarily for the differential diagnosis of breast cancer. From a medical viewpoint, diagnostic facilities for the differential cancer diagnosis should have a resolution of 3 mm or better. Because of this requirement, inverse problems of ultrasound tomography have to be solved on dense grids with sizes of up to 1000 × 1000 on cross sections of three-dimensional objects studied. Supercomputers are needed to address such inverse problems in terms of the wave model described by second-order hyperbolic equations. The algorithms developed in this study are easily scalable on supercomputers running up to several tens of thousands of processes. The problem of choosing the initial approximation for iterative algorithms when solving the inverse problem has been studied. (paper)
A Monte-Carlo-Based Network Method for Source Positioning in Bioluminescence Tomography
Zhun Xu; Xiaolei Song; Xiaomeng Zhang; Jing Bai
2007-01-01
We present an approach based on the improved Levenberg Marquardt (LM) algorithm of backpropagation (BP) neural network to estimate the light source position in bioluminescent imaging. For solving the forward problem, the table-based random sampling algorithm (TBRS), a fast Monte Carlo simulation method ...
A family of inversion formulas in thermoacoustic tomography
Nguyen, Linh
2009-10-01
We present a family of closed form inversion formulas in thermoacoustic tomography in the case of a constant sound speed. The formulas are presented in both time-domain and frequency-domain versions. As special cases, they imply most of the previously known filtered backprojection type formulas. © 2009 AMERICAN INSTITUTE OF MATHEMATICAL SCIENCES.
Purpose: A novel standalone bioluminescence and fluorescence tomography (BLT and FT) system equipped with high resolution CBCT has been built in our group. In this work, we present the system calibration method and validate our system in both phantom and in vivo environment. Methods: The CBCT is acquired by rotating the animal stage while keeping the x-ray source and detector panel static. The optical signal is reflected by the 3-mirror system to a multispectral filter set and then delivered to the CCD camera with f/1.4 lens mounted. Nine fibers passing through the stage and in contact with the mouse skin serve as the light sources for diffuse optical tomography (DOT) and FT. The anatomical information and optical properties acquired from the CBCT and DOT, respectively, are used as the priori information to improve the BLT/FT reconstruction accuracy. Flat field correction for the optical system was acquired at multiple wavelengths. A home-built phantom is used to register the optical and CBCT coordinates. An absolute calibration relating the CCD photon counts rate to the light fluence rate emitted at animal surface was developed to quantify the bioluminescence power or fluorophore concentration. Results: An optical inhomogeneous phantom with 2 light sources (3mm separation) imbedded is used to test the system. The optical signal is mapped onto the mesh generated from CBCT for optical reconstruction. Our preliminary results show that the center of mass can be reconstructed within 2.8mm accuracy. A live mouse with the light source imbedded is also used to validate our system. Liver or lung metastatic luminescence tumor model will be used for further testing. Conclusion: This hybrid system transforms preclinical research to a level that even sub-palpable volume of cells can be imaged rapidly and non-invasively, which largely extends the scope of radiobiological research. The research is supported by the NCI grant R01CA158100-01
Zhang, B; Eslami, S; Iordachita, I [Johns Hopkins University, Baltimore, Maryland (United States); Yang, Y [University of Miami School of Medicine, Miami, FL (United States); Patterson, M [Hamilton Regional Cancer Ctr., Hamilton, ON (Canada); Wong, J [Johns Hopkins University, Baltimore, MD (United States); Wang, K [Johns Hopkins Hospital, Baltimore, MD (United States)
2014-06-01
Purpose: A novel standalone bioluminescence and fluorescence tomography (BLT and FT) system equipped with high resolution CBCT has been built in our group. In this work, we present the system calibration method and validate our system in both phantom and in vivo environment. Methods: The CBCT is acquired by rotating the animal stage while keeping the x-ray source and detector panel static. The optical signal is reflected by the 3-mirror system to a multispectral filter set and then delivered to the CCD camera with f/1.4 lens mounted. Nine fibers passing through the stage and in contact with the mouse skin serve as the light sources for diffuse optical tomography (DOT) and FT. The anatomical information and optical properties acquired from the CBCT and DOT, respectively, are used as the priori information to improve the BLT/FT reconstruction accuracy. Flat field correction for the optical system was acquired at multiple wavelengths. A home-built phantom is used to register the optical and CBCT coordinates. An absolute calibration relating the CCD photon counts rate to the light fluence rate emitted at animal surface was developed to quantify the bioluminescence power or fluorophore concentration. Results: An optical inhomogeneous phantom with 2 light sources (3mm separation) imbedded is used to test the system. The optical signal is mapped onto the mesh generated from CBCT for optical reconstruction. Our preliminary results show that the center of mass can be reconstructed within 2.8mm accuracy. A live mouse with the light source imbedded is also used to validate our system. Liver or lung metastatic luminescence tumor model will be used for further testing. Conclusion: This hybrid system transforms preclinical research to a level that even sub-palpable volume of cells can be imaged rapidly and non-invasively, which largely extends the scope of radiobiological research. The research is supported by the NCI grant R01CA158100-01.
A measurement-based analytical approach to the bioluminescence tomography problem
Erkol, Hakan; Demirkiran, Aytac; Kipergil, Esra-Aytac; Uluc, Nasire; Unlu, Mehmet B.
2014-03-01
This work presents an analytical approach for the solution of the tissue diffusion equation based on the bound- ary measurements. We consider a bioluminescent point source in both homogeneous and heterogeneous circular turbid media. The point source is described by the Dirac delta function. Analytical expressions for the strength and position of the point source are obtained introducing boundary measurements and then applying appropriate boundary conditions. In addition, numerical simulations are performed for the position of the source. Calculations show that that the analytical results are in a good accordance with the numerical results.
Simultaneous inversion for velocity and attenuation by waveform tomography
Gao, Fengxia; Wang, Yanghua
2016-08-01
Seismic waveform tomography can invert for the velocity and attenuation (Q- 1) variations simultaneously. For this simultaneous inversion, we propose two strategies for waveform tomography. First, we analyze the contributions of the real part and the imaginary part of the gradients, associated with the velocity and attenuation parameters respectively, and determine that the combination of the real part of the gradient subvector for the velocity parameter and the imaginary part of the gradient subvector for the attenuation parameter would produce an optimal inversion result. Second, we attempt to balance the sensitivities of the objective function to the velocity and the attenuation parameters. Considering the magnitude differences between these two-type parameters in the simultaneous inversion, we apply preliminarily a normalization to both the velocity model and the attenuation model. However, for balancing their sensitivities, we further adjust the corresponding model updates using a tuning factor. We determine this tuning parameter adaptively, based on the sensitivities of these two parameters, at each iteration. Numerical tests demonstrate the feasibility and reliability of these two strategies in full waveform inversion.
RF Tomography for Tunnel Detection: Principles and Inversion Schemes
Lo Monte, L.; Erricolo, D.; Inan, U. S.; Wicks, M. C.
2008-12-01
We propose a novel way to detect underground tunnels based on classical seismic tomography, Ground Penetrating Radar (GPR), inverse scattering principles, and the deployment of distributed sensors, which we call "Distributed RF Tomography". Tunnel detection has been a critical problem that cannot be considered fully solved. Presently, tunnel detection is performed by methods that include seismic sensors, electrical impedance, microgravity, boreholes, and GPR. All of these methods have drawbacks that make them not applicable for use in unfriendly environments, such as battlefields. Specifically, they do not cover wide surface areas, they are generally shallow, they are limited to vertical prospecting, and require the user to be in situ, which may jeopardize one's safety. Additional application of the proposed distributed RF tomography include monitoring sensitive areas, (e.g. banks, power plants, military bases, prisons, national borders) and civil applications (e.g. environmental engineering, mine safety, search and rescue, speleology, archaeology and geophysics). The novelty of a Distributed RF tomography system consists of the following. 1) Sensors are scattered randomly above the ground, thus saving time and money compared to the use of boreholes. 2) The use of lower operating frequency (around HF), which allows for deeper penetration. 3) The use of CW diffraction tomography, which increases the resolution to sub-wavelength values, independently from the sensor displacement, and increases the SNR. 4) Use of linear inversion schemes that are suited for tunnel detection. 5) The use of modulation schemes and signal processing algorithms to mitigate interferences and noise. This presentation will cover: 1. Current physical limits of existing techniques for tunnel detection. 2. Concept of Distributed RF Tomography. 3. Inversion theories and strategies a. Proper forward model for voids buried into an homogeneous medium b. Extended matched filtering inversion c. Near
Inverse problems of ultrasound tomography in models with attenuation
We develop efficient methods for solving inverse problems of ultrasound tomography in models with attenuation. We treat the inverse problem as a coefficient inverse problem for unknown coordinate-dependent functions that characterize both the speed cross section and the coefficients of the wave equation describing attenuation in the diagnosed region. We derive exact formulas for the gradient of the residual functional in models with attenuation, and develop efficient algorithms for minimizing the gradient of the residual by solving the conjugate problem. These algorithms are easy to parallelize when implemented on supercomputers, allowing the computation time to be reduced by a factor of several hundred compared to a PC. The numerical analysis of model problems shows that it is possible to reconstruct not only the speed cross section, but also the properties of the attenuating medium. We investigate the choice of the initial approximation for iterative algorithms used to solve inverse problems. The algorithms considered are primarily meant for the development of ultrasound tomographs for differential diagnosis of breast cancer. (paper)
Simulation research on bioluminescence tomography%生物发光断层成像的仿真研究
刘勇; 齐树波; 方勇军; 陈锋
2014-01-01
目的:验证生物发光断层成像技术(bioluminescence tomography,BLT)成像的可行性并克服其成像的病态性.方法:采用BLT的前向数学模型和仿真实验结果进行分析.结果:仿真实验结果表明,基于多角度、非接触BLT成像系统(multi-view non-contact BLT imaging system),自发光源在成像体内的分布能够获得较为精确的解析,定位误差小于1 mm.结论:基于多角度、非接触的BLT成像系统,结合稀疏重建算法,能够在较少(6个)的角度下,获取较好的重建结果,有望为疾病早期诊断及药物研发等研究提供有力工具.
Chen, Xueli, E-mail: xlchen@xidian.edu.cn, E-mail: jimleung@mail.xidian.edu.cn; Zhang, Qitan; Yang, Defu; Liang, Jimin, E-mail: xlchen@xidian.edu.cn, E-mail: jimleung@mail.xidian.edu.cn [School of Life Science and Technology, Xidian University, Xi' an, Shaanxi 710071 (China)
2014-01-14
To provide an ideal solution for a specific problem of gastric cancer detection in which low-scattering regions simultaneously existed with both the non- and high-scattering regions, a novel hybrid radiosity-SP{sub 3} equation based reconstruction algorithm for bioluminescence tomography was proposed in this paper. In the algorithm, the third-order simplified spherical harmonics approximation (SP{sub 3}) was combined with the radiosity equation to describe the bioluminescent light propagation in tissues, which provided acceptable accuracy for the turbid medium with both low- and non-scattering regions. The performance of the algorithm was evaluated with digital mouse based simulations and a gastric cancer-bearing mouse based in situ experiment. Primary results demonstrated the feasibility and superiority of the proposed algorithm for the turbid medium with low- and non-scattering regions.
Bal, Guillaume; Schotland, John C
2015-01-01
We propose a method to reconstruct the density of an optical source in a highly scattering medium from ultrasound-modulated optical measurements. Our approach is based on the solution to a hybrid inverse source problem for the radiative transport equation (RTE). A controllability result for the RTE plays an essential role in the analysis.
An interactive Bayesian geostatistical inverse protocol for hydraulic tomography
Fienen, Michael N.; Clemo, Tom; Kitanidis, Peter K.
2008-01-01
Hydraulic tomography is a powerful technique for characterizing heterogeneous hydrogeologic parameters. An explicit trade-off between characterization based on measurement misfit and subjective characterization using prior information is presented. We apply a Bayesian geostatistical inverse approach that is well suited to accommodate a flexible model with the level of complexity driven by the data and explicitly considering uncertainty. Prior information is incorporated through the selection of a parameter covariance model characterizing continuity and providing stability. Often, discontinuities in the parameter field, typically caused by geologic contacts between contrasting lithologic units, necessitate subdivision into zones across which there is no correlation among hydraulic parameters. We propose an interactive protocol in which zonation candidates are implied from the data and are evaluated using cross validation and expert knowledge. Uncertainty introduced by limited knowledge of dynamic regional conditions is mitigated by using drawdown rather than native head values. An adjoint state formulation of MODFLOW-2000 is used to calculate sensitivities which are used both for the solution to the inverse problem and to guide protocol decisions. The protocol is tested using synthetic two-dimensional steady state examples in which the wells are located at the edge of the region of interest.
Zhang, Yin; Hong, Hao; Nayak, Tapas R; Valdovinos, Hector F; Myklejord, Duane V; Theuer, Charles P; Barnhart, Todd E; Cai, Weibo
2013-07-01
The goal of this study was to develop a molecular imaging agent that can allow for both positron emission tomography (PET) and near-infrared fluorescence (NIRF) imaging of CD105 expression in metastatic breast cancer. TRC105, a chimeric anti-CD105 monoclonal antibody, was labeled with both a NIRF dye (i.e., IRDye 800CW) and (64)Cu to yield (64)Cu-NOTA-TRC105-800CW. Flow cytometry analysis revealed no difference in CD105 binding affinity/specificity between TRC105 and NOTA-TRC105-800CW. Serial bioluminescence imaging (BLI) was carried out to non-invasively monitor the lung tumor burden in BALB/c mice, after intravenous injection of firefly luciferase-transfected 4T1 (i.e., fLuc-4T1) murine breast cancer cells to establish the experimental lung metastasis model. Serial PET imaging revealed that fLuc-4T1 lung tumor uptake of (64)Cu-NOTA-TRC105-800CW was 11.9 ± 1.2, 13.9 ± 3.9, and 13.4 ± 2.1 %ID/g at 4, 24, and 48 h post-injection respectively (n = 3). Biodistribution studies, blocking fLuc-4T1 lung tumor uptake with excess TRC105, control experiments with (64)Cu-NOTA-cetuximab-800CW (which served as an isotype-matched control), ex vivo BLI/PET/NIRF imaging, autoradiography, and histology all confirmed CD105 specificity of (64)Cu-NOTA-TRC105-800CW. Successful PET/NIRF imaging of tumor angiogenesis (i.e., CD105 expression) in the breast cancer experimental lung metastasis model warrants further investigation and clinical translation of dual-labeled TRC105-based agents, which can potentially enable early detection of small metastases and image-guided surgery for tumor removal. PMID:23471463
Purpose: We have developed offline and on-board bioluminescence tomography(BLT) systems for the small animal radiation research platform(SARRP) for radiation guidance of soft tissue targets. We investigated the effectiveness of offline BLT guidance. Methods: CBCT is equipped on both the offline BLT system and SARRP that are 10 ft. apart. To evaluate the setup error during animal transport between the two systems, we implanted a luminescence source in the abdomen of anesthetized mice. Five mice were studied. After CBCT was acquired on both systems, source centers and correlation coefficients were calculated. CBCT was also used to generate object mesh for BLT reconstruction. To assess target localization, we compared the localization of the luminescence source based on (1)on-board SARRP BLT and CBCT, (2)offline BLT and CBCT, and (3)offline BLT and SARRP CBCT. The 3rd comparison examines if an offline BLT system can be used to guide radiation when there is minimal target contrast in CBCT. Results: Our CBCT results show the offset of the light source center can be maintained within 0.2 mm during animal transport. The center of mass(CoM) of the light source reconstructed by the offline BLT has an offset of 1.0 ± 0.4 mm from the ‘true’ CoM as derived from the SARRP CBCT. The results compare well with the offset of 1.0 ± 0.2 mm using on-line BLT. Conclusion: With CBCT information provided by the SARRP and effective animal immobilization during transport, these findings support the use of offline BLT in close vicinity for accurate soft tissue target localization for irradiation. However, the disadvantage of the off-line system is reduced efficiency as care is required to maintain stable animal transport. We envisage a dual use system where the on-board arrangement allows convenient access to CBCT and avoids disturbance of animal setup. The off-line capability would support standalone longitudinal imaging studies. The work is supported by NIH R01CA158100 and Xstrahl
Zhang, B; Wang, K; Reyes, J; Tran, P; Wong, J [Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University, Baltimore, MD (United States); Iordachita, I [Laboratory for Computational Sensing and Robotics, Johns Hopkins University, Baltimore, MD (United States)
2015-06-15
Purpose: We have developed offline and on-board bioluminescence tomography(BLT) systems for the small animal radiation research platform(SARRP) for radiation guidance of soft tissue targets. We investigated the effectiveness of offline BLT guidance. Methods: CBCT is equipped on both the offline BLT system and SARRP that are 10 ft. apart. To evaluate the setup error during animal transport between the two systems, we implanted a luminescence source in the abdomen of anesthetized mice. Five mice were studied. After CBCT was acquired on both systems, source centers and correlation coefficients were calculated. CBCT was also used to generate object mesh for BLT reconstruction. To assess target localization, we compared the localization of the luminescence source based on (1)on-board SARRP BLT and CBCT, (2)offline BLT and CBCT, and (3)offline BLT and SARRP CBCT. The 3rd comparison examines if an offline BLT system can be used to guide radiation when there is minimal target contrast in CBCT. Results: Our CBCT results show the offset of the light source center can be maintained within 0.2 mm during animal transport. The center of mass(CoM) of the light source reconstructed by the offline BLT has an offset of 1.0 ± 0.4 mm from the ‘true’ CoM as derived from the SARRP CBCT. The results compare well with the offset of 1.0 ± 0.2 mm using on-line BLT. Conclusion: With CBCT information provided by the SARRP and effective animal immobilization during transport, these findings support the use of offline BLT in close vicinity for accurate soft tissue target localization for irradiation. However, the disadvantage of the off-line system is reduced efficiency as care is required to maintain stable animal transport. We envisage a dual use system where the on-board arrangement allows convenient access to CBCT and avoids disturbance of animal setup. The off-line capability would support standalone longitudinal imaging studies. The work is supported by NIH R01CA158100 and Xstrahl
Sadikot, Ruxana T.; Blackwell, Timothy S.
2005-01-01
Bioluminescence refers to the process of visible light emission in living organisms. Bioluminescence imaging is a powerful methodology that has been developed over the last decade as a tool for molecular imaging of small laboratory animals, enabling the study of ongoing biological processes in vivo. This form of optical imaging is low cost and noninvasive and facilitates real-time analysis of disease processes at the molecular level in living organisms. In this article, we provide a brief int...
Scattered Neutron Tomography Based on A Neutron Transport Inverse Problem
William Charlton
2007-07-01
Neutron radiography and computed tomography are commonly used techniques to non-destructively examine materials. Tomography refers to the cross-sectional imaging of an object from either transmission or reflection data collected by illuminating the object from many different directions.
Inverse problem of Ocean Acoustic Tomography (OAT) - A numerical experiment
Murty, T.V.R.; Somayajulu, Y.K.; Mahadevan, R.; Murty, C.S.
the correctness of the solution. In the stochastic inverse case, for random model parameter and data, the vertical structure of the ocean is modeled through the quasi-geostrophic theory while the horizontal structure is assumed to have Gaussian covariance...
Destabilized bioluminescent proteins
Allen, Michael S.; Rakesh, Gupta; Gary, Sayler S.
2007-07-31
Purified nucleic acids, vectors and cells containing a gene cassette encoding at least one modified bioluminescent protein, wherein the modification includes the addition of a peptide sequence. The duration of bioluminescence emitted by the modified bioluminescent protein is shorter than the duration of bioluminescence emitted by an unmodified form of the bioluminescent protein.
Inverse problems in vision and 3D tomography
Mohamad-Djafari, Ali
2013-01-01
The concept of an inverse problem is a familiar one to most scientists and engineers, particularly in the field of signal and image processing, imaging systems (medical, geophysical, industrial non-destructive testing, etc.) and computer vision. In imaging systems, the aim is not just to estimate unobserved images, but also their geometric characteristics from observed quantities that are linked to these unobserved quantities through the forward problem. This book focuses on imagery and vision problems that can be clearly written in terms of an inverse problem where an estimate for the image a
Refraction traveltime tomography with irregular topography using the unwrapped phase inversion
Choi, Yun Seok
2013-01-01
Traveltime tomography has long served as a stable and efficient tool for velocity estimation, especially for the near surface. It, however, suffers from some of limitations associated with ray tracing and high-frequency traveltime in velocity inversion zones and ray shadow regions. We develop a tomographic approach based on traveltime solutions obtained by tracking the phase (instantaneous traveltime) of the wavefield solution of the Helmholtz wave equation. Since the instantaneous-traveltime does not suffer from phase wrapping, the inversion algorithm using the instantaneous-traveltime has the potential to generate robust inversion results. With a high damping factor, the instantaneous-traveltime inversion provides refraction tomography similar results, but from a single frequency. Despite the Helmholtz-based solver implementation, the tomographic inversion handles irrgular topography. The numerical examples show that our inversion algorithm generates a convergent smooth velocity model, which looks very much like a tomographic result. Next, we plan to apply the instantaneous-traveltime inversion algorithm to real seismic data acquired from the near surface with irregular topography.
Inversion methods for fast-ion velocity-space tomography in fusion plasmas
Jacobsen, Asger Schou; Stagner, L.; Salewski, Mirko;
2016-01-01
Velocity-space tomography has been used to infer 2D fast-ion velocity distribution functions. Here we compare the performance of five different tomographic inversion methods: truncated singular value decomposition, maximum entropy, minimum Fisher information and zeroth and first-order Tikhonov re...
Brocher, T. M.; Parsons, T.; Blakely, R. J.
2001-12-01
We present a simultaneous seismic tomography and gravity inversion model for the subsurface geometry of Tertiary basins underlying the Puget Lowland, Washington. The method extrapolates high-resolution seismic tomography results from Seismic Hazards Investigation of Puget Sound (SHIPS), which covered much of the Lowland, to adjacent regions not well imaged by SHIPS. Our current algorithm uses the initial seismic tomography result to calculate the gravity field assuming Gardner's rule of ρ (kg/m3) = 1740v0.25 for velocities (in km/s) below 6 km/s. We currently use ρ = 2920 kg/m3 for velocities greater than 6 km/s. Iteratively, the method compares the observed and calculated gravity fields, increases or decreases the velocity gradient as necessary, and updates the velocity model for the next iteration of the seismic tomography inversion. This tomography result is subsequently used for another comparison of observed and calculated gravity fields. Currently, the RMS first-arrival travel time misfit (90 msec) produced by this algorithm is identical to that obtained using solely the seismic data, and the RMS gravity error is 9 mgal, slightly higher than desired. Nonetheless, the simultaneous inversion has successfully extended the region of subsurface coverage from that obtained from SHIPS to the core of the accretionary rocks on the Olympic Peninsula and to the Everett and Bellingham basins, where the SHIPS coverage was limited. The inverse model clearly shows accretionary rocks in the Olympic core complex dipping eastward beneath east dipping rocks of the Siletz terrane. We present an overview of our algorithm and summarize the crustal structure inferred from our inversion.
Tomography of the ionospheric electron density with geostatistical inversion
Minkwitz, D.; van den Boogaart, K. G.; Gerzen, T.; Hoque, M.
2015-08-01
In relation to satellite applications like global navigation satellite systems (GNSS) and remote sensing, the electron density distribution of the ionosphere has significant influence on trans-ionospheric radio signal propagation. In this paper, we develop a novel ionospheric tomography approach providing the estimation of the electron density's spatial covariance and based on a best linear unbiased estimator of the 3-D electron density. Therefore a non-stationary and anisotropic covariance model is set up and its parameters are determined within a maximum-likelihood approach incorporating GNSS total electron content measurements and the NeQuick model as background. As a first assessment this 3-D simple kriging approach is applied to a part of Europe. We illustrate the estimated covariance model revealing the different correlation lengths in latitude and longitude direction and its non-stationarity. Furthermore, we show promising improvements of the reconstructed electron densities compared to the background model through the validation of the ionosondes Rome, Italy (RO041), and Dourbes, Belgium (DB049), with electron density profiles for 1 day.
Wang, Kun; Anis, Fatima; Li, Cuiping; Duric, Neb; Anastasio, Mark A
2015-01-01
Ultrasound computed tomography (USCT) holds great promise for improving the detection and management of breast cancer. Because they are based on the acoustic wave equation, waveform inversion-based reconstruction methods can produce images that possess improved spatial resolution properties over those produced by ray-based methods. However, waveform inversion methods are computationally demanding and have not been applied widely in USCT breast imaging. In this work, source encoding concepts are employed to develop an accelerated USCT reconstruction method that circumvents the large computational burden of conventional waveform inversion methods. This method, referred to as the waveform inversion with source encoding (WISE) method, encodes the measurement data using a random encoding vector and determines an estimate of the sound speed distribution by solving a stochastic optimization problem by use of a stochastic gradient descent algorithm. Both computer-simulation and experimental phantom studies are conduc...
Hermand, Jean-Pierre; Berrada, Mohamed; Meyer, Matthias; Asch, Mark
2005-09-01
Recently, an analytic adjoint-based method of optimal nonlocal boundary control has been proposed for inversion of a waveguide acoustic field using the wide-angle parabolic equation [Meyer and Hermand, J. Acoust. Soc. Am. 117, 2937-2948 (2005)]. In this paper a numerical extension of this approach is presented that allows the direct inversion for the geoacoustic parameters which are embedded in a spectral integral representation of the nonlocal boundary condition. The adjoint model is generated numerically and the inversion is carried out jointly across multiple frequencies. The paper further discusses the application of the numerical adjoint PE method for ocean acoustic tomography. To show the effectiveness of the implemented numerical adjoint, preliminary inversion results of water sound-speed profile and bottom acoustic properties will be shown for the YELLOW SHARK '94 experimental conditions.
Zhang, Yin; Hong, Hao; Nayak, Tapas R.; Valdovinos, Hector F.; Myklejord, Duane V.; Theuer, Charles P.; Barnhart, Todd E.; Cai, Weibo
2013-01-01
The goal of this study was to develop a molecular imaging agent that can allow for both positron emission tomography (PET) and near-infrared fluorescence (NIRF) imaging of CD105 expression in metastatic breast cancer. TRC105, a chimeric anti-CD105 monoclonal antibody, was labeled with both a NIRF dye (i.e., IRDye 800CW) and 64Cu to yield 64Cu-NOTA-TRC105-800CW. Flow cytometry analysis revealed no difference in CD105 binding affinity/specificity between TRC105 and NOTA-TRC105-800CW. Serial bio...
Silva Neto, Antonio Jose da [Universidade do Estado, Nova Friburgo, RJ (Brazil). Inst. Politecnico; Roberty, Nilson Costa [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia. Programa de Engenharia Nuclear
1998-07-01
A brief description of the mathematical modeling of tomography with radiation scattering is given. The direct problem is modeled by the Boltzmann Transport Equation. For the inverse problem the source-detector approach is used. (author)
Gehre, Matthias, E-mail: mgehre@math.uni-bremen.de [Center for Industrial Mathematics, University of Bremen, Bremen D-28344 (Germany); Jin, Bangti, E-mail: bangti.jin@gmail.com [Department of Mathematics, University of California, Riverside, University Ave. 900, Riverside, CA 92521 (United States)
2014-02-15
In this paper, we study a fast approximate inference method based on expectation propagation for exploring the posterior probability distribution arising from the Bayesian formulation of nonlinear inverse problems. It is capable of efficiently delivering reliable estimates of the posterior mean and covariance, thereby providing an inverse solution together with quantified uncertainties. Some theoretical properties of the iterative algorithm are discussed, and the efficient implementation for an important class of problems of projection type is described. The method is illustrated with one typical nonlinear inverse problem, electrical impedance tomography with complete electrode model, under sparsity constraints. Numerical results for real experimental data are presented, and compared with that by Markov chain Monte Carlo. The results indicate that the method is accurate and computationally very efficient.
Time-dependent stochastic inversion (TDSI) was recently developed for acoustic travel-time tomography of the atmosphere. This type of tomography allows reconstruction of temperature and wind-velocity fields given the location of sound sources and receivers and the travel times between all source–receiver pairs. The quality of reconstruction provided by TDSI depends on the geometry of the transducer array. However, TDSI has not been studied for the geometry with reciprocal sound transmission. This paper is focused on three aspects of TDSI. First, the use of TDSI in reciprocal sound transmission arrays is studied in numerical and physical experiments. Second, efficiency of time-dependent and ordinary stochastic inversion (SI) algorithms is studied in numerical experiments. Third, a new model of noise in the input data for TDSI is developed that accounts for systematic errors in transducer positions. It is shown that (i) a separation of the travel times into temperature and wind-velocity components in tomography with reciprocal transmission does not improve the reconstruction, (ii) TDSI yields a better reconstruction than SI and (iii) the developed model of noise yields an accurate reconstruction of turbulent fields and estimation of errors in the reconstruction
Diagnostic and operational tasks in dental radiology often require three-dimensional information that is difficult or impossible to see in a projection image. A CT-scan provides the dentist with comprehensive three-dimensional data. However, often CT-scan is impractical and, instead, only a few projection radiographs with sparsely distributed projection directions are available. Statistical (Bayesian) inversion is well-suited approach for reconstruction from such incomplete data. In statistical inversion, a priori information is used to compensate for the incomplete information of the data. The inverse problem is recast in the form of statistical inference from the posterior probability distribution that is based on statistical models of the projection data and the a priori information of the tissue. In this paper, a statistical model for three-dimensional imaging of dentomaxillofacial structures is proposed. Optimization and MCMC algorithms are implemented for the computation of posterior statistics. Results are given with in vitro projection data that were taken with a commercial intraoral x-ray sensor. Examples include limited-angle tomography and full-angle tomography with sparse projection data. Reconstructions with traditional tomographic reconstruction methods are given as reference for the assessment of the estimates that are based on the statistical model
An investigation on the solutions for the linear inverse problem in gamma ray tomography
This paper the results obtained in single beam gamma ray tomography are investigated according to direct problem formulation and the applied solution for the linear system of equations. By image reconstruction based algebraic computational algorithms are used. The sparse under and over-determined linear system of equations was analyzed. Build in functions of Matlab software were applied and optimal solutions were investigate. Experimentally a section of the tube is scanned from various positions and at different angles. The solution, to find the vector of coefficients μ, from the vector of measured p values through the W matrix inversion, constitutes an inverse problem. A industrial tomography process requires a numerical solution of the system of equations. The definition of inverse problem according to Hadmard's is considered and as well the requirement of a well posed problem to find stable solutions. The formulation of the basis function and the computational algorithm to structure the weight matrix W were analyzed. For W full rank matrix the obtained solution is unique as expected. Total Least Squares was implemented which theory and computation algorithm gives adequate treatment for the problems due to non-unique solutions of the system of equations. Stability of the solution was investigating by means of a regularization technique and the comparison shows that it improves the results. An optimal solution as a function of the image quality, computation time and minimum residuals were quantified. The corresponding reconstructed images are shown in 3D graphics in order to compare with the solution. (author)
Inversion methods for fast-ion velocity-space tomography in fusion plasmas
Jacobsen, A. S.; Stagner, L.; Salewski, M.; Geiger, B.; Heidbrink, W. W.; Korsholm, S. B.; Leipold, F.; Nielsen, S. K.; Rasmussen, J.; Stejner, M.; Thomsen, H.; Weiland, M.; the ASDEX Upgrade Team
2016-04-01
Velocity-space tomography has been used to infer 2D fast-ion velocity distribution functions. Here we compare the performance of five different tomographic inversion methods: truncated singular value decomposition, maximum entropy, minimum Fisher information and zeroth- and first-order Tikhonov regularization. The inversion methods are applied to fast-ion {{\\text{D}}α} measurements taken just before and just after a sawtooth crash in the ASDEX Upgrade tokamak as well as to synthetic measurements from different test distributions. We find that the methods regularizing by penalizing steep gradients or maximizing entropy perform best. We assess the uncertainty of the calculated inversions taking into account photon noise, uncertainties in the forward model as well as uncertainties introduced by the regularization which allows us to distinguish regions of high and low confidence in the tomographies. In high confidence regions, all methods agree that ions with pitch values close to zero, as well as ions with large pitch values, are ejected from the plasma center by the sawtooth crash, and that this ejection depletes the ion population with large pitch values more strongly.
Efficient non-negative constrained model-based inversion in optoacoustic tomography
Ding, Lu; Luís Deán-Ben, X.; Lutzweiler, Christian; Razansky, Daniel; Ntziachristos, Vasilis
2015-09-01
The inversion accuracy in optoacoustic tomography depends on a number of parameters, including the number of detectors employed, discrete sampling issues or imperfectness of the forward model. These parameters result in ambiguities on the reconstructed image. A common ambiguity is the appearance of negative values, which have no physical meaning since optical absorption can only be higher or equal than zero. We investigate herein algorithms that impose non-negative constraints in model-based optoacoustic inversion. Several state-of-the-art non-negative constrained algorithms are analyzed. Furthermore, an algorithm based on the conjugate gradient method is introduced in this work. We are particularly interested in investigating whether positive restrictions lead to accurate solutions or drive the appearance of errors and artifacts. It is shown that the computational performance of non-negative constrained inversion is higher for the introduced algorithm than for the other algorithms, while yielding equivalent results. The experimental performance of this inversion procedure is then tested in phantoms and small animals, showing an improvement in image quality and quantitativeness with respect to the unconstrained approach. The study performed validates the use of non-negative constraints for improving image accuracy compared to unconstrained methods, while maintaining computational efficiency.
Kubina, Filip; Moczo, Peter; Kristek, Jozef; Michlik, Filip
2016-04-01
Adjoint tomography has proven an irreplaceable useful tool in exploring Earth's structure in the regional and global scales. It has not been widely applied for improving models of local surface sedimentary structures (LSSS) in numerical predictions of earthquake ground motion (EGM). Anomalous earthquake motions and corresponding damage in earthquakes are often due to site effects in local surface sedimentary basins. Because majority of world population is located atop surface sedimentary basins, it is important to predict EGM at these sites during future earthquakes. A major lesson learned from dedicated international tests focused on numerical prediction of EGM in LSSS is that it is hard to reach better agreement between data and synthetics without an improved structural model. If earthquake records are available for sites atop a LSSS it is natural to consider them for improving the structural model. Computationally efficient adjoint tomography might be a proper tool. A seismic wavefield in LSSS is relatively very complex due to diffractions, conversions, interference and often also resonant phenomena. In shallow basins, the first arrivals are not suitable for inversion due to almost vertical incidence and thus insufficient vertical resolution. Later wavefield consists mostly of local surface waves often without separated wave groups. Consequently, computed kernels are complicated and not suitable for inversion without pre-processing. The spatial complexity of a kernel can be dramatic in a typical situation with relatively low number of sources (local earthquakes) and surface receivers. This complexity can be simplified by directionally-dependent smoothing and spatially-dependent normalization that condition reasonable convergence. A multiscale approach seems necessary given the usual difference between the available and true models. Interestingly, only a successive inversion of μ and λ elastic moduli, and different scale sequences lead to good results.
Optical coherence tomography signal analysis: LIDAR like equation and inverse methods
Optical Coherence Tomography (OCT) is based on the media backscattering properties in order to obtain tomographic images. In a similar way, LIDAR (Light Detection and Range) technique uses these properties to determine atmospheric characteristics, specially the signal extinction coefficient. Exploring this similarity allowed the application of signal inversion methods to the OCT images, allowing to construct images based in the extinction coefficient, original result until now. The goal of this work was to study, propose, develop and implement algorithms based on OCT signal inversion methodologies with the aim of determine the extinction coefficient as a function of depth. Three inversion methods were used and implemented in LABViewR: slope, boundary point and optical depth. Associated errors were studied and real samples (homogeneous and stratified) were used for two and three dimension analysis. The extinction coefficient images obtained from the optical depth method were capable to differentiate air from the sample. The images were studied applying PCA and cluster analysis that established the methodology strength in determining the sample's extinction coefficient value. Moreover, the optical depth methodology was applied to study the hypothesis that there is some correlation between signal extinction coefficient and the enamel teeth demineralization during a cariogenic process. By applying this methodology, it was possible to observe the variation of the extinction coefficient as depth function and its correlation with microhardness variation, showing that in deeper layers its values tends to a healthy tooth values, behaving as the same way that the microhardness. (author)
CMT Source Inversions for Massive Data Assimilation in Global Adjoint Tomography
Lei, W.; Ruan, Y.; Bozdag, E.; Lefebvre, M. P.; Smith, J. A.; Modrak, R. T.; Komatitsch, D.; Song, X.; Liu, Q.; Tromp, J.; Peter, D. B.
2015-12-01
Full Waveform Inversion (FWI) is a vital tool for probing the Earth's interior and enhancing our knowledge of the underlying dynamical processes [e.g., Liu et al., 2012]. Using the adjoint tomography method, we have successfully obtained a first-generation global FWI model named M15 [Bozdag et al., 2015]. To achieve higher resolution of the emerging new structural features and to accommodate azimuthal anisotropy and anelasticity in the next-generation model, we expanded our database from 256 to 4,224 earthquakes. Previous studies have shown that ray-theory-based Centroid Moment Tensor (CMT) inversion algorithms can produce systematic biases in earthquake source parameters due to tradeoffs with 3D crustal and mantle heterogeneity [e.g., Hjorleifsdottir et al., 2010]. To reduce these well-known tradeoffs, we performed CMT inversions in our current 3D global model before resuming the structural inversion with the expanded database. Initial source parameters are selected from the global CMT database [Ekstrom et al., 2012], with moment magnitudes ranging from 5.5 to 7.0 and occurring between 1994 and 2015. Data from global and regional networks were retrieved from the IRIS DMC. Synthetic seismograms were generated based on the spectral-element-based seismic wave propagation solver (SPECFEM3D GLOBE) in model M15. We used a source inversion algorithm based on a waveform misfit function while allowing time shifts between data and synthetics to accommodate additional unmodeled 3D heterogeneity [Liu et al., 2004]. To accommodate the large number of earthquakes and time series (more than 10,000,000 records), we implemented a source inversion workflow based on the newly developed Adaptive Seismic Data Format (ASDF) [Krischer, Smith, et al., 2015] and ObsPy [Krischer et al., 2015]. In ASDF, each earthquake is associated with a single file, thereby eliminating I/O bottlenecks in the workflow and facilitating fast parallel processing. Our preliminary results indicate that errors
Measurements and Kernels for Source-Structure Inversions in Noise Tomography
Hanasoge, Shravan M
2013-01-01
Seismic noise cross correlations are used to image crustal structure and heterogeneity. Typically, seismic networks are only anisotropically illuminated by seismic noise, a consequence of the non-uniform distribution of sources. Here, we study the sensitivity of such a seismic network to structural heterogeneity in a 2-D setting. We compute finite-frequency cross-correlation sensitivity kernels for travel-time, waveform-energy and waveform-difference measurements. In line with expectation, wavespeed anomalies are best imaged using travel times and the source distribution using cross-correlation energies. Perturbations in attenuation and impedance are very difficult to image and reliable inferences require a high degree of certainty in the knowledge of the source distribution and wavespeed model (at least in the case of transmission tomography studied here). We perform single-step Gauss-Newton inversions for the source distribution and the wavespeed, in that order, and quantify the associated Cram\\'{e}r-Rao lo...
Hosseini-zad, K.; Stähler, S. C.; Sigloch, K.; Scheingraber, C.
2012-04-01
Seismic tomography has made giant progresses in the last decade. This has been due to improvements in the method, which allowed to combine the high information content of waveform modeling with the mathematically sound methods of tomographic inversion. The second factor is the vast growth of digitally available broadband seismograms. Both factors together require efficient processing schemes for seismic waveforms, which reduce the necessary manual interaction to a minimum. Since the data growth has mainly taken place on traditionally well instrumented regions, many areas are still sparsely instrumented, so the processing scheme should treat all data with highest care. Our processing scheme "No data left behind", which is implemented in Python and incorporated into the seismology package ObsPy automates the steps for global or regional body wave tomography: 1. Data retrieval: Downloading of event-based seismic waveforms from ORFEUS and IRIS. This way around 1600 stations globally are available. Data from other sources can be added manually. 2. Preprocessing: Deconvolution of instrument responses, recognition of bad recordings and automated correction, if possible. No rejection is done in this stage. 3. Cutting of time windows around body wave phases, decomposition of the signals into 6 frequency bands (20s to 1 Hz), individual determination of SNR and similarity to synthetic waveforms. 4. Rejection of bad windows. Since the rejection is done based on SNR or CC with synthetics independently for each of the 6 frequency bands, even very noisy stations like ocean islands are not discarded completely. 5. Bayesian Source inversion: The source parameters including depth, CMT and Source Time Function are determined in a probabilistic way using a wavelet base and P- and SH-waveforms. The whole algorithm is modular and additional modules (e.g. for OBS preprocessing) can be selected individually.
Optimisation of acquisition time in bioluminescence imaging
Taylor, Shelley L.; Mason, Suzannah K. G.; Glinton, Sophie; Cobbold, Mark; Styles, Iain B.; Dehghani, Hamid
2015-03-01
Decreasing the acquisition time in bioluminescence imaging (BLI) and bioluminescence tomography (BLT) will enable animals to be imaged within the window of stable emission of the bioluminescent source, a higher imaging throughput and minimisation of the time which an animal is anaesthetised. This work investigates, through simulation using a heterogeneous mouse model, two methods of decreasing acquisition time: 1. Imaging at fewer wavelengths (a reduction from five to three); and 2. Increasing the bandwidth of filters used for imaging. The results indicate that both methods are viable ways of decreasing the acquisition time without a loss in quantitative accuracy. Importantly, when choosing imaging wavelengths, the spectral attenuation of tissue and emission spectrum of the source must be considered, in order to choose wavelengths at which a high signal can be achieved. Additionally, when increasing the bandwidth of the filters used for imaging, the bandwidth must be accounted for in the reconstruction algorithm.
From tomography to full-waveform inversion with a single objective function
Alkhalifah, Tariq Ali
2014-02-17
In full-waveform inversion (FWI), a gradient-based update of the velocity model requires an initial velocity that produces synthetic data that are within a half-cycle, everywhere, from the field data. Such initial velocity models are usually extracted from migration velocity analysis or traveltime tomography, among other means, and are not guaranteed to adhere to the FWI requirements for an initial velocity model. As such, we evaluated an objective function based on the misfit in the instantaneous traveltime between the observed and modeled data. This phase-based attribute of the wavefield, along with its phase unwrapping characteristics, provided a frequency-dependent traveltime function that was easy to use and quantify, especially compared to conventional phase representation. With a strong Laplace damping of the modeled, potentially low-frequency, data along the time axis, this attribute admitted a first-arrival traveltime that could be compared with picked ones from the observed data, such as in wave equation tomography (WET). As we relax the damping on the synthetic and observed data, the objective function measures the misfit in the phase, however unwrapped. It, thus, provided a single objective function for a natural transition from WET to FWI. A Marmousi example demonstrated the effectiveness of the approach.
The approximate inversion as a reconstruction method in X-ray computerized tomography
Dietz, R L
1999-01-01
The mathematical model of the X-ray computerized tomography will be developed in the first chapter, the approximate inversion will be introduced, and the Radon Transform will be used as an example to demonstrate calculation of a reconstruction cone. In the second chapter, a reconstruction method for the parallel geometry is discussed, leading to derivation of the method for a fan-beam geometry. The approximate inversion calculated for the limited-angle case is presented as an example of incomplete data problems. As with complete data problems, numerical examples are given and the method is compared with existing other methods. 3D reconstruction is the topic of the third chapter. Although of no relevance in practice, a parallel geometry will be examined. No problems are encountered in transferring the reconstruction cone to the cone beam geometry, but only for a scanning curve which also is of no relevance in practice. A further reconstruction method is presented for curves fulfilling the so-called Tuy conditi...
State space regularization in the nonstationary inverse problem for diffuse optical tomography
In this paper, we present a regularization method in the nonstationary inverse problem for diffuse optical tomography (DOT). The regularization is based on a choosing time evolution process such that in a stationary state it has a covariance function which corresponds to a process with similar smoothness properties as the first-order smoothness Tikhonov regularization. The proposed method is computationally more lightweight than the method where the regularization is augmented as a measurement. The method was tested in the case of the inverse problem of DOT. A solid phantom with optical properties similar to tissue was made, incorporating two moving parts that simulate two different physiological processes: a localized change in absorption and a surrounding rotating two-part shell which simulates slow oscillations in the tissue background physiology. A sequence of measurements of the phantom was made and the reconstruction of the image sequence was computed using this method. It allows the recovery of the full time series of images from relatively slow measurements with one source active at a time. In practice, this allows instruments with a larger dynamic range to be applied to the imaging of functional phenomena using DOT
Li, Guo; Xia, Jun; Li, Lei; Wang, Lidai; Wang, Lihong V.
2015-03-01
Linear transducer arrays are readily available for ultrasonic detection in photoacoustic computed tomography. They offer low cost, hand-held convenience, and conventional ultrasonic imaging. However, the elevational resolution of linear transducer arrays, which is usually determined by the weak focus of the cylindrical acoustic lens, is about one order of magnitude worse than the in-plane axial and lateral spatial resolutions. Therefore, conventional linear scanning along the elevational direction cannot provide high-quality three-dimensional photoacoustic images due to the anisotropic spatial resolutions. Here we propose an innovative method to achieve isotropic resolutions for three-dimensional photoacoustic images through combined linear and rotational scanning. In each scan step, we first elevationally scan the linear transducer array, and then rotate the linear transducer array along its center in small steps, and scan again until 180 degrees have been covered. To reconstruct isotropic three-dimensional images from the multiple-directional scanning dataset, we use the standard inverse Radon transform originating from X-ray CT. We acquired a three-dimensional microsphere phantom image through the inverse Radon transform method and compared it with a single-elevational-scan three-dimensional image. The comparison shows that our method improves the elevational resolution by up to one order of magnitude, approaching the in-plane lateral-direction resolution. In vivo rat images were also acquired.
Proximal methods for the resolution of inverse problems: application to positron emission tomography
The objective of this work is to propose reliable, efficient and fast methods for minimizing convex criteria, that are found in inverse problems for imagery. We focus on restoration/reconstruction problems when data is degraded with both a linear operator and noise, where the latter is not assumed to be necessarily additive.The reliability of the method is ensured through the use of proximal algorithms, the convergence of which is guaranteed when a convex criterion is considered. Efficiency is sought through the choice of criteria adapted to the noise characteristics, the linear operators and the image specificities. Of particular interest are regularization terms based on total variation and/or sparsity of signal frame coefficients. As a consequence of the use of frames, two approaches are investigated, depending on whether the analysis or the synthesis formulation is chosen. Fast processing requirements lead us to consider proximal algorithms with a parallel structure. Theoretical results are illustrated on several large size inverse problems arising in image restoration, stereoscopy, multi-spectral imagery and decomposition into texture and geometry components. We focus on a particular application, namely Positron Emission Tomography (PET), which is particularly difficult because of the presence of a projection operator combined with Poisson noise, leading to highly corrupted data. To optimize the quality of the reconstruction, we make use of the spatio-temporal characteristics of brain tissue activity. (author)
Lehikoinen, A.; Huttunen, J.M.J.; Finsterle, S.; Kowalsky, M.B.; Kaipio, J.P.
2009-08-01
We propose an approach for imaging the dynamics of complex hydrological processes. The evolution of electrically conductive fluids in porous media is imaged using time-lapse electrical resistance tomography. The related dynamic inversion problem is solved using Bayesian filtering techniques, that is, it is formulated as a sequential state estimation problem in which the target is an evolving posterior probability density of the system state. The dynamical inversion framework is based on the state space representation of the system, which involves the construction of a stochastic evolution model and an observation model. The observation model used in this paper consists of the complete electrode model for ERT, with Archie's law relating saturations to electrical conductivity. The evolution model is an approximate model for simulating flow through partially saturated porous media. Unavoidable modeling and approximation errors in both the observation and evolution models are considered by computing approximate statistics for these errors. These models are then included in the construction of the posterior probability density of the estimated system state. This approximation error method allows the use of approximate - and therefore computationally efficient - observation and evolution models in the Bayesian filtering. We consider a synthetic example and show that the incorporation of an explicit model for the model uncertainties in the state space representation can yield better estimates than a frame-by-frame imaging approach.
The Toast++ software suite for forward and inverse modeling in optical tomography.
Schweiger, Martin; Arridge, Simon
2014-04-01
We present the Toast++ open-source software environment for solving the forward and inverse problems in diffuse optical tomography (DOT). The software suite consists of a set of libraries to simulate near-infrared light propagation in highly scattering media with complex boundaries and heterogeneous internal parameter distribution, based on a finite-element solver. Steady-state, time- and frequency-domain data acquisition systems can be modeled. The forward solver is implemented in C++ and supports performance acceleration with parallelization for shared and distributed memory architectures, as well as graphics processing computation. Building on the numerical forward solver, Toast++ contains model-based iterative inverse solvers for reconstructing the volume distribution of absorption and scattering parameters from boundary measurements of light transmission. A range of regularization methods are provided, including the possibility of incorporating prior knowledge of internal structure. The user can link to the Toast++ libraries either directly to compile application programs for DOT, or make use of the included MATLAB and PYTHON bindings to generate script-based solutions. This approach allows rapid prototyping and provides a rich toolset in both environments for debugging, testing, and visualization. PMID:24781586
A robust probabilistic approach for variational inversion in shallow water acoustic tomography
This paper presents a variational methodology for inverting shallow water acoustic tomography (SWAT) measurements. The aim is to determine the vertical profile of the speed of sound c(z), knowing the acoustic pressures generated by a frequency source and collected by a sparse vertical hydrophone array (VRA). A variational approach that minimizes a cost function measuring the distance between observations and their modeled equivalents is used. A regularization term in the form of a quadratic restoring term to a background is also added. To avoid inverting the variance–covariance matrix associated with the above-weighted quadratic background, this work proposes to model the sound speed vector using probabilistic principal component analysis (PPCA). The PPCA introduces an optimum reduced number of non-correlated latent variables η, which determine a new control vector and a new regularization term, expressed as ηTη. The PPCA represents a rigorous formalism for the use of a priori information and allows an efficient implementation of the variational inverse method
Focusing inversion techniques applied to electrical resistance tomography in an experimental tank
Pagliara, G
2006-01-01
We present an algorithm for focusing inversion of electrical resistivity tomography (ERT) data. ERT is a typical example of ill-posed problem. Regularization is the most common way to face this kind of problems; it basically consists in using a priori information about targets to reduce the ambiguity and the instability of the solution. By using the minimum gradient support (MGS) stabilizing functional, we introduce the following geometrical prior information in the reconstruction process: anomalies have sharp boundaries. The presented work is embedded in a project (L.A.R.A.) which aims at the estimation of hydrogeological properties from geophysical investigations. L.A.R.A. facilities include a simulation tank (4 m x 8 m x 1.35 m); 160 electrodes are located all around the tank and used for 3-D ERT. Because of the large number of electrodes and their dimensions, it is important to model their effect in order to correctly evaluate the electrical system response. The forward modelling in the presented algorith...
Surface waves tomography and non-linear inversion in the southeast Carpathians
A set of shear-wave velocity models of the lithosphere-asthenosphere system in the southeast Carpathians is determined by the non-linear inversion of surface wave group velocity data, obtained from a tomographic analysis. The local dispersion curves are assembled for the period range 7 s - 150 s, combining regional group velocity measurements and published global Rayleigh wave dispersion data. The lithosphere-asthenosphere velocity structure is reliably reconstructed to depths of about 250 km. The thickness of the lithosphere in the region varies from about 120 km to 250 km and the depth of the asthenosphere between 150 km and 250 km. Mantle seismicity concentrates where the high velocity lid is detected just below the Moho. The obtained results are in agreement with recent seismic refraction, receiver function, and travel time P-wave tomography investigations in the region. The similarity among the results obtained from different kinds of structural investigations (including the present work) highlights some new features of the lithosphere-asthenosphere system in southeast Carpathians, as the relatively thin crust under Transylvania basin and Vrancea zone. (author)
Yi, Ji; Backman, Vadim
2012-01-01
We here develop a method to measure and image the full optical scattering properties by inverse spectroscopic optical coherence tomography (ISOCT). Tissue is modelled as a medium with continuous refractive index (RI) fluctuation and such a fluctuation is described by the RI correlation functions. Under the first-order Born approximation, the forward model is established for ISOCT. By measuring optical quantities of tissue including the scattering power (SP) of the OCT spectrum, the reflection...
Yi, Ji; Radosevich, Andrew J.; Stypula-Cyrus, Yolanda; Nikhil N Mutyal; Azarin, Samira Michelle; Horcher, Elizabeth; Goldberg, Michael J.; Bianchi, Laura K.; Bajaj, Shailesh; Hemant K. Roy; Backman, Vadim
2014-01-01
Abstract. Field carcinogenesis is the initial stage of cancer progression. Understanding field carcinogenesis is valuable for both cancer biology and clinical medicine. Here, we used inverse spectroscopic optical coherence tomography to study colorectal cancer (CRC) and pancreatic cancer (PC) field carcinogenesis. Depth-resolved optical and ultrastructural properties of the mucosa were quantified from histologically normal rectal biopsies from patients with and without colon adenomas ( n = 85...
We make a multiscale investigation of the lithosphere-asthenosphere structure and of the active tectonics along a stripe from the Tyrrhenian to the Adriatic coast, with emphasis on the Umbria-Marche area, by means of surface-wave tomography and inversion experiments for structure and seismic moment tensor retrieval. The data include: a large number of new local and regional group velocity measurements sampling the Umbria-Marche Apennines and the Adria margin respectively; new and published phase velocity measurements sampling Italy and surroundings; deep seismic soundings which, crossing the whole Peninsula from the Tyrrhenian to the Adriatic coasts, go through the Umbria-Marche area. The local group velocity maps cover the area reactivated by the 1997-1998 Umbria-Marche earthquake sequence. These maps suggest an intimate relation between the lateral variations and distribution of the active fault systems and related sedimentary basins. Such relation is confirmed by the non-linear inversion of the local dispersion curves. To image the structure of the lithosphere-asthenosphere system from the Tyrrhenian to the Adriatic coast, we fix the upper crust parameters consistently with our Umbria-Marche models and with pertinent deep seismic sounding data and invert the regional long period dispersion measurements. At a local scale, in the Umbria-Marche area, the retrieved models for the upper crust reveal the importance of the inherited compressional tectonics on the ongoing extensional deformation and related seismic activity. The lateral and in-depth structural changes in the upper crust are likely controlling fault segmentation and seismogenesis. Source inversion studies of the large crustal events of the 1997 earthquake sequence show the dominance of normal faulting mechanisms, whereas selected aftershocks between the fault segments reveal that the prevailing deformation at the step-over is of strike-slip faulting type and may control the lateral fault extent. At the
Hansen, Thomas Mejer; Cordua, Knud Skou; Holm Jacobsen, Bo;
2014-01-01
tested for two synthetic ground-penetrating radar crosshole tomographic inverse problems. Ignoring the modeling error can lead to severe artifacts, which erroneously appear to be well resolved in the solution of the inverse problem. Accounting for the modeling error leads to a solution of the inverse...
U-SPECT-BioFluo: an integrated radionuclide, bioluminescence, and fluorescence imaging platform
Van Oosterom, M.N.; Kreuger, R.; Buckle, T.; Mahn, W.A.; Bunschoten, A.; Josephson, L.; Van Leeuwen, F.W.B.; Beekman, F.J.
2014-01-01
Background: In vivo bioluminescence, fluorescence, and single-photon emission computed tomography (SPECT) imaging provide complementary information about biological processes. However, to date these signatures are evaluated separately on individual preclinical systems. In this paper, we introduce a
HT2DINV: A 2D forward and inverse code for steady-state and transient hydraulic tomography problems
Soueid Ahmed, A.; Jardani, A.; Revil, A.; Dupont, J. P.
2015-12-01
Hydraulic tomography is a technique used to characterize the spatial heterogeneities of storativity and transmissivity fields. The responses of an aquifer to a source of hydraulic stimulations are used to recover the features of the estimated fields using inverse techniques. We developed a 2D free source Matlab package for performing hydraulic tomography analysis in steady state and transient regimes. The package uses the finite elements method to solve the ground water flow equation for simple or complex geometries accounting for the anisotropy of the material properties. The inverse problem is based on implementing the geostatistical quasi-linear approach of Kitanidis combined with the adjoint-state method to compute the required sensitivity matrices. For undetermined inverse problems, the adjoint-state method provides a faster and more accurate approach for the evaluation of sensitivity matrices compared with the finite differences method. Our methodology is organized in a way that permits the end-user to activate parallel computing in order to reduce the computational burden. Three case studies are investigated demonstrating the robustness and efficiency of our approach for inverting hydraulic parameters.
Xing, Guangchi; Niu, Fenglin; Chen, Min; Yang, Yingjie
2016-05-01
Surface wave tomography routinely uses empirically scaled density model in the inversion of dispersion curves for shear wave speeds of the crust and uppermost mantle. An improperly selected empirical scaling relationship between density and shear wave speed can lead to unrealistic density models beneath certain tectonic formations such as sedimentary basins. Taking the Sichuan basin east to the Tibetan plateau as an example, we investigate the differences between density profiles calculated from four scaling methods and their effects on Rayleigh wave phase velocities. Analytical equations for 1-D layered models and adjoint tomography for 3-D models are used to examine the trade-off between density and S-wave velocity structures at different depth ranges. We demonstrate that shallow density structure can significantly influence phase velocities at short periods, and thereby affect the shear wave speed inversion from phase velocity data. In particular, a deviation of 25 per cent in the initial density model can introduce an error up to 5 per cent in the inverted shear velocity at middle and lower crustal depths. Therefore one must pay enough attention in choosing a proper velocity-density scaling relationship in constructing initial density model in Rayleigh wave inversion for crustal shear velocity structure.
Yi, Ji; Backman, Vadim
2012-11-01
We here develop a method to measure and image the full optical scattering properties by inverse spectroscopic optical coherence tomography (ISOCT). Tissue is modelled as a medium with continuous refractive index (RI) fluctuation and such a fluctuation is described by the RI correlation functions. Under the first-order Born approximation, the forward model is established for ISOCT. By measuring optical quantities of tissue including the scattering power of the OCT spectrum, the reflection albedo α defined as the ratio of scattering coefficient μ(s), and the backscattering coefficient μ(b), we are able to inversely deduce the RI correlation function and image the full set of optical scattering properties. PMID:23114323
Hansen, Thomas Mejer; Cordua, Knud Skou; Holm Jacobsen, Bo;
2014-01-01
Inversion of geophysical data relies on knowledge about how to solve the forward problem, that is, computing data from a given set of model parameters. In many applications of inverse problems, the solution to the forward problem is assumed to be known perfectly, without any error. In reality, so...
Ahmed, A. Soueid; Jardani, A.; Revil, A.; Dupont, J. P.
2016-03-01
Transient hydraulic tomography is used to image the heterogeneous hydraulic conductivity and specific storage fields of shallow aquifers using time series of hydraulic head data. Such ill-posed and non-unique inverse problem can be regularized using some spatial geostatistical characteristic of the two fields. In addition to hydraulic heads changes, the flow of water, during pumping tests, generates an electrical field of electrokinetic nature. These electrical field fluctuations can be passively recorded at the ground surface using a network of non-polarizing electrodes connected to a high impedance (> 10 MOhm) and sensitive (0.1 mV) voltmeter, a method known in geophysics as the self-potential method. We perform a joint inversion of the self-potential and hydraulic head data to image the hydraulic conductivity and specific storage fields. We work on a 3D synthetic confined aquifer and we use the adjoint state method to compute the sensitivities of the hydraulic parameters to the hydraulic head and self-potential data in both steady-state and transient conditions. The inverse problem is solved using the geostatistical quasi-linear algorithm framework of Kitanidis. When the number of piezometers is small, the record of the transient self-potential signals provides useful information to characterize the hydraulic conductivity and specific storage fields. These results show that the self-potential method reveals the heterogeneities of some areas of the aquifer, which could not been captured by the tomography based on the hydraulic heads alone. In our analysis, the improvement on the hydraulic conductivity and specific storage estimations were based on perfect knowledge of electrical resistivity field. This implies that electrical resistivity will need to be jointly inverted with the hydraulic parameters in future studies and the impact of its uncertainty assessed with respect to the final tomograms of the hydraulic parameters.
Joint inversion of muon tomography and gravimetry - a resolving kernel approach
Jourde, Kevin; Marteau, Jacques
2014-01-01
Both muon tomography and gravimetry are geophysical methods that provide information on the density structure of the Earth's subsurface. Muon tomography measures the natural flux of cosmic muons and its attenuation produced by the screening effect of the rock mass to image. Gravimetry generally consists in measurements of the vertical component of the local gravity field. Both methods are linearly linked to density, but their spatial sensitivity is very different. Muon tomography essentially works like medical X-ray scan and integrates density information along elongated narrow conical volumes while gravimetry measurements are linked to density by a 3-dimensional integral encompassing the whole studied domain. We develop the mathematical expressions of these integration formulas -- called acquisition kernels -- to express resolving kernels that act as spatial filters relating the true unknown density structure to the density distribution actually recoverable from the available data. The resolving kernels prov...
Numerical solution of 2D-vector tomography problem using the method of approximate inverse
Svetov, Ivan; Maltseva, Svetlana; Polyakova, Anna
2016-08-01
We propose a numerical solution of reconstruction problem of a two-dimensional vector field in a unit disk from the known values of the longitudinal and transverse ray transforms. The algorithm is based on the method of approximate inverse. Numerical simulations confirm that the proposed method yields good results of reconstruction of vector fields.
Pustelnik, N.
2010-12-15
The objective of this work is to propose reliable, efficient and fast methods for minimizing convex criteria, that are found in inverse problems for imagery. We focus on restoration/reconstruction problems when data is degraded with both a linear operator and noise, where the latter is not assumed to be necessarily additive.The reliability of the method is ensured through the use of proximal algorithms, the convergence of which is guaranteed when a convex criterion is considered. Efficiency is sought through the choice of criteria adapted to the noise characteristics, the linear operators and the image specificities. Of particular interest are regularization terms based on total variation and/or sparsity of signal frame coefficients. As a consequence of the use of frames, two approaches are investigated, depending on whether the analysis or the synthesis formulation is chosen. Fast processing requirements lead us to consider proximal algorithms with a parallel structure. Theoretical results are illustrated on several large size inverse problems arising in image restoration, stereoscopy, multi-spectral imagery and decomposition into texture and geometry components. We focus on a particular application, namely Positron Emission Tomography (PET), which is particularly difficult because of the presence of a projection operator combined with Poisson noise, leading to highly corrupted data. To optimize the quality of the reconstruction, we make use of the spatio-temporal characteristics of brain tissue activity. (author)
BIOLUMINESCENCE IMAGING: PROGRESS AND APPLICATIONS
Badr, Christian E.; Tannous, Bakhos A
2011-01-01
Application of bioluminescence imaging has grown tremendously in the past decade and has significantly contributed to the core conceptual advances in biomedical research. This technology provides valuable means for monitoring of different biological processes for immunology, oncology, virology and neuroscience. In this review, we will discuss current trends in bioluminescence and its application in different fields with emphasis on cancer research.
Afanasiev, M.; Pratt, R. G.; Kamei, R.; McDowell, G.
2012-12-01
Crosshole seismic tomography has been used by Vale to provide geophysical images of mineralized massive sulfides in the Eastern Deeps deposit at Voisey's Bay, Labrador, Canada. To date, these data have been processed using traveltime tomography, and we seek to improve the resolution of these images by applying acoustic Waveform Tomography. Due to the computational cost of acoustic waveform modelling, local descent algorithms are employed in Waveform Tomography; due to non-linearity an initial model is required which predicts first-arrival traveltimes to within a half-cycle of the lowest frequency used. Because seismic velocity anisotropy can be significant in hardrock settings, the initial model must quantify the anisotropy in order to meet the half-cycle criterion. In our case study, significant velocity contrasts between the target massive sulfides and the surrounding country rock led to difficulties in generating an accurate anisotropy model through traveltime tomography, and our starting model for Waveform Tomography failed the half-cycle criterion at large offsets. We formulate a new, semi-global approach for finding the best-fit 1-D elliptical anisotropy model using simulated annealing. Through random perturbations to Thompson's ɛ parameter, we explore the L2 norm of the frequency-domain phase residuals in the space of potential anisotropy models: If a perturbation decreases the residuals, it is always accepted, but if a perturbation increases the residuals, it is accepted with the probability P = exp(-(Ei-E)/T). This is the Metropolis criterion, where Ei is the value of the residuals at the current iteration, E is the value of the residuals for the previously accepted model, and T is a probability control parameter, which is decreased over the course of the simulation via a preselected cooling schedule. Convergence to the global minimum of the residuals is guaranteed only for infinitely slow cooling, but in practice good results are obtained from a variety
Bioluminescent bacteria: lux genes as environmental biosensors
Nunes-Halldorson Vânia da Silva; Duran Norma Letícia
2003-01-01
Bioluminescent bacteria are widespread in natural environments. Over the years, many researchers have been studying the physiology, biochemistry and genetic control of bacterial bioluminescence. These discoveries have revolutionized the area of Environmental Microbiology through the use of luminescent genes as biosensors for environmental studies. This paper will review the chronology of scientific discoveries on bacterial bioluminescence and the current applications of bioluminescence in env...
Time stamp generation with inverse FIR filters for Positron Emission Tomography
Photon coincidence detection is the process by which Positron Emission Tomography (PET) works. This requires the determination of the time of impact of each coincident photon at the detector system, also known as time stamp. In this work, the timestamp was generated by means of digital time-domain deconvolution with FIR filters for a INa(Tl) based system. The detector deadtime was reduced from 350 ns to 175 ns while preserving the system's energy resolution and a direct relation between the amount of light collected and the temporal resolution was found.(author)
U-SPECT-BioFluo: an integrated radionuclide, bioluminescence, and fluorescence imaging platform
2014-01-01
Background In vivo bioluminescence, fluorescence, and single-photon emission computed tomography (SPECT) imaging provide complementary information about biological processes. However, to date these signatures are evaluated separately on individual preclinical systems. In this paper, we introduce a fully integrated bioluminescence-fluorescence-SPECT platform. Next to an optimization in logistics and image fusion, this integration can help improve understanding of the optical imaging (OI) resul...
A geometric calibration method for inverse geometry computed tomography using P-matrices
Slagowski, Jordan M.; Dunkerley, David A. P.; Hatt, Charles R.; Speidel, Michael A.
2016-03-01
Accurate and artifact free reconstruction of tomographic images requires precise knowledge of the imaging system geometry. This work proposes a novel projection matrix (P-matrix) based calibration method to enable C-arm inverse geometry CT (IGCT). The method is evaluated for scanning-beam digital x-ray (SBDX), a C-arm mounted inverse geometry fluoroscopic technology. A helical configuration of fiducials is imaged at each gantry angle in a rotational acquisition. For each gantry angle, digital tomosynthesis is performed at multiple planes and a composite image analogous to a cone-beam projection is generated from the plane stack. The geometry of the C-arm, source array, and detector array is determined at each angle by constructing a parameterized 3D-to-2D projection matrix that minimizes the sum-of-squared deviations between measured and projected fiducial coordinates. Simulations were used to evaluate calibration performance with translations and rotations of the source and detector. In a geometry with 1 mm translation of the central ray relative to the axis-of-rotation and 1 degree yaw of the detector and source arrays, the maximum error in the recovered translational parameters was 0.4 mm and maximum error in the rotation parameter was 0.02 degrees. The relative rootmean- square error in a reconstruction of a numerical thorax phantom was 0.4% using the calibration method, versus 7.7% without calibration. Changes in source-detector-distance were the most challenging to estimate. Reconstruction of experimental SBDX data using the proposed method eliminated double contour artifacts present in a non-calibrated reconstruction. The proposed IGCT geometric calibration method reduces image artifacts when uncertainties exist in system geometry.
Koulakov, Ivan; Burov, Evgeniy; Cloetingh, Sierd; El Khrepy, Sami; Al-Arifi, Nassir; Bushenkova, Natalia
2016-01-01
We present a new model of P-velocity anomalies in the upper mantle beneath the Arabian Peninsula, Red Sea, and surrounding regions. This model was computed with the use of travel time data from the global catalogue of the International Seismological Center (ISC) for the years of 1980-2011. The reliability of the model was tested with several synthetic tests. In the resulting seismic model, the Red Sea is clearly associated with a higher P-velocity anomaly in the upper mantle at least down to 300 km depth. This anomaly might be caused by upward deviation of the main mantle interfaces caused by extension and thinning of the lithosphere due to passive rifting. Thick lithosphere of the Arabian Platform is imaged as a high-velocity anomaly down to 200-250 km depth. Below this plate, we observe a low-velocity structure that is interpreted as a hot mantle upwelling. Based on the tomography results, we propose that this upper mantle anomaly may represent hot material that migrates westward and play a major role in the formation of Cenozoic basaltic lava fields in western Arabia. On the northeastern side of the Arabian Plate, we clearly observe a dipping high-velocity zone beneath Zagros and Makran, which is interpreted as a trace of subduction or delamination of the Arabian Plate lithosphere.
Chemiluminescence and bioluminescence microbe detection
Taylor, R. E.; Chappelle, E.; Picciolo, G. L.; Jeffers, E. L.; Thomas, R. R.
1978-01-01
Automated biosensors for online use with NASA Water Monitoring System employs bioluminescence and chemiluminescence techniques to rapidly measure microbe contamination of water samples. System eliminates standard laboratory procedures requiring time duration of 24 hours or longer.
C. Eva
1994-06-01
Full Text Available In this paper we apply various inversion methods to a set of teleseismic data collected by a network operating along the Ligurian Belt in the transition region between Alps and Apennines. In particular, we consider the regularization method, the truncated singular value decomposition, the Landweber method (with the Related Simultaneous Iterative Reconstruction Technique and the conjugate gradient method. All the methods provide rather similar velocity models which are well approximated by that provided by back-projection (used with an appropriate normalization constant. A drawback of these models seems to be the large discrepancy (of the order of 40% between the observed time residuals and those computed from the model itself. However, for each station of the network, the azimuth dependence of the computed time residuals reproduces rather well the observed one so that it is believable that the most significant information contained in the data has been expIoited. The computed velocity models indicate strong heterogeneities in the first 200 km below the Apennines.
D. Papanastassiou
1997-06-01
Full Text Available The three-dimensional attenuation structure beneath the Aegean sea and the surrounding regions was determined by inversion of seismic intensity data. A large number of seismic intensity data have been accumulated in a uniform scale in the Aegean region, where the seismic activity is much higher than that of the other Mediterranean regions. Nearly 11000 seismic intensity data from 47 earthquakes that have occurred in these regions were used to determine the seismic attenuation structure. The resulting structure reveals a remarkable contrast of attenuation. In the top layer (depth 0-20 km, low Q is dominant in the central Aegean sea, while high Q is dominant in the surrounding land areas, except for Southwestern Turkey. The low-Q regions correspond to areas of Neogene-Quaternary grabens where the high seismicity of shallow earthquakes appears. In the lower layer (20-40 km low-Q areas are located in the southeastern part of the Hellenic arc. Some low-Q spots corresponding to the distribution of volcanoes exist along the volcanic arc. The low-Q spots might correspond to diapirs causing subduction volcanism.
SU-C-207-01: Four-Dimensional Inverse Geometry Computed Tomography: Concept and Its Validation
Purpose: In past few years, the inverse geometry computed tomography (IGCT) system has been developed to overcome shortcomings of a conventional computed tomography (CT) system such as scatter problem induced from large detector size and cone-beam artifact. In this study, we intend to present a concept of a four-dimensional (4D) IGCT system that has positive aspects above all with temporal resolution for dynamic studies and reduction of motion artifact. Methods: Contrary to conventional CT system, projection data at a certain angle in IGCT was a group of fractionated narrow cone-beam projection data, projection group (PG), acquired from multi-source array which have extremely short time gap of sequential operation between each of sources. At this, for 4D IGCT imaging, time-related data acquisition parameters were determined by combining multi-source scanning time for collecting one PG with conventional 4D CBCT data acquisition sequence. Over a gantry rotation, acquired PGs from multi-source array were tagged time and angle for 4D image reconstruction. Acquired PGs were sorted into 10 phase and image reconstructions were independently performed at each phase. Image reconstruction algorithm based upon filtered-backprojection was used in this study. Results: The 4D IGCT had uniform image without cone-beam artifact on the contrary to 4D CBCT image. In addition, the 4D IGCT images of each phase had no significant artifact induced from motion compared with 3D CT. Conclusion: The 4D IGCT image seems to give relatively accurate dynamic information of patient anatomy based on the results were more endurable than 3D CT about motion artifact. From this, it will be useful for dynamic study and respiratory-correlated radiation therapy. This work was supported by the Industrial R&D program of MOTIE/KEIT [10048997, Development of the core technology for integrated therapy devices based on real-time MRI guided tumor tracking] and the Mid-career Researcher Program (2014R1A2A1A
SU-C-207-01: Four-Dimensional Inverse Geometry Computed Tomography: Concept and Its Validation
Kim, K; Kim, D; Kim, T; Kang, S; Cho, M; Shin, D; Suh, T [The Catholic University of Korea, Seoul (Korea, Republic of)
2015-06-15
Purpose: In past few years, the inverse geometry computed tomography (IGCT) system has been developed to overcome shortcomings of a conventional computed tomography (CT) system such as scatter problem induced from large detector size and cone-beam artifact. In this study, we intend to present a concept of a four-dimensional (4D) IGCT system that has positive aspects above all with temporal resolution for dynamic studies and reduction of motion artifact. Methods: Contrary to conventional CT system, projection data at a certain angle in IGCT was a group of fractionated narrow cone-beam projection data, projection group (PG), acquired from multi-source array which have extremely short time gap of sequential operation between each of sources. At this, for 4D IGCT imaging, time-related data acquisition parameters were determined by combining multi-source scanning time for collecting one PG with conventional 4D CBCT data acquisition sequence. Over a gantry rotation, acquired PGs from multi-source array were tagged time and angle for 4D image reconstruction. Acquired PGs were sorted into 10 phase and image reconstructions were independently performed at each phase. Image reconstruction algorithm based upon filtered-backprojection was used in this study. Results: The 4D IGCT had uniform image without cone-beam artifact on the contrary to 4D CBCT image. In addition, the 4D IGCT images of each phase had no significant artifact induced from motion compared with 3D CT. Conclusion: The 4D IGCT image seems to give relatively accurate dynamic information of patient anatomy based on the results were more endurable than 3D CT about motion artifact. From this, it will be useful for dynamic study and respiratory-correlated radiation therapy. This work was supported by the Industrial R&D program of MOTIE/KEIT [10048997, Development of the core technology for integrated therapy devices based on real-time MRI guided tumor tracking] and the Mid-career Researcher Program (2014R1A2A1A
Circular polarization observed in bioluminescence
Wijnberg, Hans; Meijer, E.W.; Hummelen, J.C.; Dekkers, H.P.J.M.; Schippers, P.H.; Carlson, A.D.
1980-01-01
While investigating circular polarization in luminescence, and having found it in chemiluminescence, we have studied bioluminescence because it is such a widespread and dramatic natural phenomenon. We report here that left and right lanterns of live larvae of the fireflies, Photuris lucicrescens and
Tomography is a non-intrusive imaging technique being developed at CRNL as an industrial tool for generating quantitative cross-sectional density maps of objects. Of most interest is tomography's ability to: distinguish features within complex geometries where other NDT techniques fail because of the complexity of the geometry; detect/locate small density changes/defects within objects, e.g. void fraction measurements within thick-walled vessels, shrink cavities in castings, etc.; provide quantitative data that can be used in analyses, e.g. of complex processes, or fracture mechanics; and provide objective quantitative data that can be used for (computer-based) quality assurance decisions, thereby reducing and in some cases eliminating the present subjectivity often encountered in NDT. The CRNL program is reviewed and examples are presented to illustrate the potential and the limitations of the technology
Bioluminescence imaging in live cells and animals.
Tung, Jack K; Berglund, Ken; Gutekunst, Claire-Anne; Hochgeschwender, Ute; Gross, Robert E
2016-04-01
The use of bioluminescent reporters in neuroscience research continues to grow at a rapid pace as their applications and unique advantages over conventional fluorescent reporters become more appreciated. Here, we describe practical methods and principles for detecting and imaging bioluminescence from live cells and animals. We systematically tested various components of our conventional fluorescence microscope to optimize it for long-term bioluminescence imaging. High-resolution bioluminescence images from live neurons were obtained with our microscope setup, which could be continuously captured for several hours with no signs of phototoxicity. Bioluminescence from the mouse brain was also imaged noninvasively through the intact skull with a conventional luminescence imager. These methods demonstrate how bioluminescence can be routinely detected and measured from live cells and animals in a cost-effective way with common reagents and equipment. PMID:27226972
Pasquet, Sylvain; BODET, Ludovic; Longuevergne, Laurent; Dhemaied, Amine; Camerlynck, Christian; REJIBA, Fayçal; Guérin, Roger
2015-01-01
International audience The joint study of pressure (P-) and shear (S-) wave velocities (Vp and Vs ), as well as their ratio (Vp /Vs), has been used for many years at large scales but remains marginal in near-surface applications. For these applications, and are generally retrieved with seismic refraction tomography combining P and SH (shear-horizontal) waves, thus requiring two separate acquisitions. Surface-wave prospecting methods are proposed here as an alternative to SH-wave tomography...
Protein-protein complexation in bioluminescence
Titushin, Maxim S.; Feng, Yingang; Lee, John; Vysotski, Eugene S.; Liu, Zhi-jie
2011-01-01
In this review we summarize the progress made towards understanding the role of protein-protein interactions in the function of various bioluminescence systems of marine organisms, including bacteria, jellyfish and soft corals, with particular focus on methodology used to detect and characterize these interactions. In some bioluminescence systems, protein-protein interactions involve an “accessory protein” whereby a stored substrate is efficiently delivered to the bioluminescent enzyme lucife...
A Nisin Bioassay Based on Bioluminescence
Wahlström, G.; Saris, P. E. J.
1999-01-01
A Lactococcus lactis subsp. lactis strain that can sense the bacteriocin nisin and transduce the signal into bioluminescence was constructed. By using this strain, a bioassay based on bioluminescence was developed for quantification of nisin, for detection of nisin in milk, and for identification of nisin-producing strains. As little as 0.0125 ng of nisin per ml was detected within 3 h by this bioluminescence assay. This detection limit was lower than in previously described methods.
Murty, T.V.R.; Rao, M.M.M.; Sadhuram, Y.
corresponding to the predicted ray arrivals were identified and travel time perturbations of the most stable Eigen rays enabled reconstruction of temperature anomaly from the sound velocity perturbations using stochastic inverse method. For formulation...
Liu, Xin; Zhao, Dapeng
2016-03-01
We determined P and S wave velocity tomography of the Japan subduction zone down to a depth of 700 km by conducting joint inversions of a large number of high-quality arrival-time data of local earthquakes and teleseismic events which are newly collected for this study. We also determined 2-D phase-velocity images of fundamental mode Rayleigh waves at periods of 20-150 s beneath Japan and the surrounding oceanic regions using amplitude and phase data of teleseismic Rayleigh waves. A detailed 3-D S-wave tomography of the study region is obtained by jointly inverting S-wave arrival times of local and teleseismic events and the Rayleigh-wave phase-velocity data. Our inversion results reveal the subducting Pacific and Philippine Sea slabs clearly as dipping high-velocity zones from a 1-D starting velocity model. Prominent low-velocity (low-V) anomalies are revealed in the mantle wedge above the slabs and in the mantle below the Pacific slab. The distinct velocity contrasts between the subducting slabs and the surrounding mantle reflect significant lateral variations in temperature as well as water content and/or the degree of partial melting. The low-V anomalies in the mantle wedge are attributed to slab dehydration and corner flows in the mantle wedge. A sheet-like low-V zone is revealed under the Pacific slab beneath NE Japan, which may reflect hot upwelling from the deeper mantle and subduction of a plume-fed asthenosphere as well. Our present results indicate that joint inversions of different seismic data are very effective and important for obtaining robust tomographic images of the crust and mantle.
Yokota, T.; Miyazaki, T. [Geological Survey of Japan, Tsukuba (Japan); Rokugawa, S.; Matsushima, J. [The University of Tokyo, Tokyo (Japan). Faculty of Engineering; Ashida, Y. [Kyoto University, Kyoto (Japan). Faculty of Engineering
1996-10-01
In the case where sources and receivers are not distributed on a 2-D plane, seismic tomography inversion was studied. In tomography experiments, the existing wells are generally used. In such case, sources and receivers are frequently not distributed on a 2-D plane. The 2.5-D analysis method including 2-D structure and 3-D ray-tracing was thus developed. This method is featured by less memory necessary for ray-tracing calculation, and the same algorithm for velocity determination as 2-D analysis method. In previous methods, since analysis is generally carried out by projecting sources and receivers on a certain assumed 2-D plane, it can derive correct results in the case of constant velocity and straight ray, however, in the other case, it derives incorrect results. Application of 3-D tomography requires a large amount of memory, and falls into poor convergence because of various parameters. The 2.5-D analysis method can avoid these demerits. This analysis method was applied to the data obtained in Ogiri area, Kagoshima prefecture. 5 refs., 3 figs., 2 tabs.
Hu, R.; Brauchler, R.; Herold, M.; Bayer, P.; Sauter, M.
2009-04-01
Rarely is it possible to draw a significant conclusion about the geometry and the properties of geological structures of the underground using the information which is typically obtained from boreholes, since soil exploration is only representative of the position where the soil sample is taken from. Conventional aquifer investigation methods like pumping tests can provide hydraulic properties of a larger area; however, they lead to integral information. This information is insufficient to develop groundwater models, especially contaminant transport models, which require information about the spatial distribution of the hydraulic properties of the subsurface. Hydraulic tomography is an innovative method which has the potential to spatially resolve three dimensional structures of natural aquifer bodies. The method employs hydraulic short term tests performed between two or more wells, whereby the pumped intervals (sources) and the observation points (receivers) are separated by double packer systems. In order to optimize the computationally intensive tomographic inversion of transient hydraulic data we have decided to couple two inversion approaches (a) hydraulic travel time inversion and (b) steady shape inversion. (a) Hydraulic travel time inversion is based on the solution of the travel time integral, which describes the relationship between travel time of maximum signal variation of a transient hydraulic signal and the diffusivity between source and receiver. The travel time inversion is computationally extremely effective and robust, however, it is limited to the determination of diffusivity. In order to overcome this shortcoming we use the estimated diffusivity distribution as starting model for the steady shape inversion with the goal to separate the estimated diffusivity distribution into its components, hydraulic conductivity and specific storage. (b) The steady shape inversion utilizes the fact that at steady shape conditions, drawdown varies with time but
Munzarova, H.; Plomerova, J.; Kissling, E. H.
2015-12-01
Consideration of only isotropic wave propagation and neglecting anisotropy in tomography studies is a simplification obviously incongruous with current understanding of mantle-lithosphere plate dynamics. Both fossil anisotropy in the mantle lithosphere and anisotropy due to the present-day flow in the asthenosphere may significantly influence propagation of seismic waves. We present a novel code for anisotropic teleseismic tomography (AniTomo) that allows to invert relative P-wave travel time residuals simultaneously for coupled isotropic-anisotropic P-wave velocity models of the upper mantle. We have modified frequently-used isotropic teleseismic tomography code Telinv by assuming weak hexagonal anisotropy with symmetry axis oriented generally in 3D to be, together with heterogeneities, a source of the observed P-wave travel-time residuals. Careful testing of the new code with synthetics, concentrating on strengths and limitations of the inversion method, is a necessary step before AniTomo is applied to real datasets. We examine various aspects of anisotropic tomography and particularly influence of ray coverage on resolvability of individual model parameters and of initial models on the result. Synthetic models are designed to schematically represent heterogeneous and anisotropic structures in the upper mantle. Several synthetic tests mimicking a real tectonic setting, e.g. the lithosphere subduction in the Northern Apennines in Italy (Munzarova et al., G-Cubed, 2013), allow us to make quantitative assessments of the well-known trade-off between effects of seismic anisotropy and heterogeneities. Our results clearly document that significant distortions of imaged velocity heterogeneities may result from neglecting anisotropy.
Tomography images of a body are constructed by placing a plurality of surface electrodes at spaced intervals on the body, causing currents to flow in the body (e.g. by applying a potential between each pair of electrodes in turn, or by induction), and measuring the potential between pairs of electrodes, calculating the potential expected in each case on the assumption that the body consists of a medium of uniform impedance, plotting the isopotentials corresponding to the calculated results to create a uniform image of the body, obtaining the ratio between the measured potential and the calculated potential in each case, and modifying the image in accordance with the respective ratios by increasing the assumed impedance along an isopotential in proportion to a ratio greater than unity or decreasing the assumed impedance in proportion to a ratio less than unity. The modified impedances along the isopotentials for each pair of electrodes are superimposed. The calculations are carried out using a computer and the plotting is carried out by a visual display unit and/or a print-out unit. (author)
REVIEW OF ENVIRONMENTAL APPLICATIONS OF BIOLUMINESCENCE MEASUREMENTS
This review of the recent literature on environmental applications of bioluminescence systems will focus on in vivo and in vitro bioluminescence methods that have been utilized to elucidate properties of chemicals, toxic and mutagenic effects, and to estimate biomass. he unifying...
Bioluminescence imaging characteristics and application
Bioluminescence imaging (BLI) by luciferase gene marked cells or DNA, in the presence of ATP and oxygen, catalytic oxidation reaction of fluorescein luminescence. So that it can directly monitor in vivo cell activity and gene behavior. In this paper, by comparing the BLI and MRI, PET, radiography of the similarities and differences, as well as about their cancer, stem cells and immune cells transportation, apoptosis and other aspects of the application, in order to better provide the basis for promoting the application of BLI. (authors)
Understanding bioluminescence in dinoflagellates — how far have we come?
Martha Valiadi; Debora Iglesias-Rodriguez
2013-01-01
Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to the organisms’ lifestyle. In this paper, we review the literature on the cellular mechanisms, molecular evolution, diversity, and ecology of bioluminescence ...
Three-dimensional localization of in vivo bioluminescent source based on multispectral imaging
Feng, Jinchao; Jia, Kebin; Tian, Jie; Yan, Guorui; Zhu, Shouping
2009-02-01
Bioluminescence tomography (BLT) is a novel in vivo technique in small animal studies, which can reveal the molecular and cellular information at the whole-body small animal level. At present, there is an increasing interest in multispectral bioluminescence tomography, since multispectral data acquisition could improve the BLT performance significantly. In view to the ill-posedness of BLT problem, we develop an optimal permissible source region strategy to constrain the possible solution of the source by utilizing spectrum character of bioluminescent source. Then a linear system to link the measured data with the unknown light source variables is established by utilizing the optimal permissible region strategy based on adaptive finite element analysis. Furthermore, singular value decomposition analysis is used for data dimensionality reduction and improving computational efficiency in multispectral case. The reconstructed speed and stability benefit from adaptive finite element, the permissible region strategy and singular value decomposition. In the numerical simulation, the heterogeneous phantom experiment has been used to evaluate the performance of the proposed algorithm with the Monte Carlo based synthetic data. The reconstruction results demonstrate the merits and potential of our methodology for localizing bioluminescent source.
Inversion techniques in the Soft X-Ray tomography of fusion plasmas: towards real-time applications
Mlynář, Jan; Weinzettl, Vladimír; Bonheure, G.; Murari, A.
2010-01-01
Roč. 58, č. 3 (2010), s. 733-741. ISSN 1536-1055. [Workshop on Fusion Data Processing, Validation and Ananlyses/6th./. Madrid, 25.01.2010-27.01.2010] R&D Projects: GA ČR GAP205/10/2055; GA ČR GA202/09/1467; GA MŠk LA08048 Institutional research plan: CEZ:AV0Z20430508 Keywords : plasma tomography * real-time control * soft-X-ray diagnostics Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 0.654, year: 2010 http://www.new.ans.org/store/j_10922
Daniel, Ramiz; Almog, Ronen; Ron, Amit; Belkin, Shimshon; Diamand, Yosi Shacahm
2008-12-01
Whole-cell biosensors are potential candidates for on-line and in situ environmental monitoring. In this work we present a new design of a whole-cell bioluminescence biosensor for water toxicity detection, based on genetically engineered Escherichia coli bacteria, carrying a recA::luxCDABE promoter-reporter fusion. Sensitive optical detection is achieved using a single photon avalanche photodiode (SPAD) working in the Geiger mode. The present work describes a simple mathematical model for the kinetic process of the bioluminescence based SOS toxin response of E. coli bacteria. We find that initially the bioluminescence signal depends on the time square and we show that the spectral intensity of the bioluminescence signal is inverse proportional to the frequency. We get excellent agreement between the theoretical model and the measured light signal. Furthermore, we present experimental results of the bioluminescent signal measurement using a SPAD and a photomultiplier, and demonstrate improvement of the measurement by applying a matched digital filter. Low intensity bioluminescence signals were measured after the whole-cell sensors were exposed to various toxicant concentrations (5, 15 and 20ppm). PMID:18774705
Analytical Applications of Bioluminescence and Chemiluminescence
Chappelle, E. W. (Editor); Picciolo, G. L. (Editor)
1975-01-01
Bioluminescence and chemiluminescence studies were used to measure the amount of adenosine triphosphate and therefore the amount of energy available. Firefly luciferase - luciferin enzyme system was emphasized. Photometer designs are also considered.
Repeated and Widespread Evolution of Bioluminescence in Marine Fishes.
Davis, Matthew P; Sparks, John S; Smith, W Leo
2016-01-01
Bioluminescence is primarily a marine phenomenon with 80% of metazoan bioluminescent genera occurring in the world's oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication. PMID:27276229
Repeated and Widespread Evolution of Bioluminescence in Marine Fishes
Davis, Matthew P.; Sparks, John S.; Smith, W. Leo
2016-01-01
Bioluminescence is primarily a marine phenomenon with 80% of metazoan bioluminescent genera occurring in the world’s oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication. PMID:27276229
Circadian Control Sheds Light on Fungal Bioluminescence
Oliveira, Anderson G.; Cassius V. Stevani; Waldenmaier, Hans E.; Viviani, Vadim; Emerson, Jillian M.; Loros, Jennifer J.; Jay C Dunlap
2015-01-01
Bioluminescence, the creation and emission of light by organisms, affords insight into the lives of organisms doing it. Luminous living things are widespread and access diverse mechanisms to generate and control luminescence [1-5]. Among the least studied bioluminescent organisms are phylogenetically rare fungi – only 71 species, all within the ~9000 fungi of the temperate and tropical Agaricales Order - are reported from among ~100,000 described fungal species [6,7]. All require oxygen [8] a...
MEASUREMENTS OF BIOLUMINESCENCE IN DEEP SEA
Chikawa, M.; Kitamura, T; Nakagawa, Nakagawa; Yamamoto, I.; Wada, T.; Okei, K; Yamashita, Y.
1996-01-01
[Abstract] We have designed and built a photon counting system which measures low intensities of bioluminescence in deep sea. The system comprises a CCD-TV camera, two-dimensional image intensifier and video cassette recorder. Using this system we measured the vertical profile of bioluminescence in situ at the Suruga Trough and Nankai Trough to a depth of 3600 m and analyzed cultivated them.
Noninvasive Bioluminescence Imaging in Small Animals
Zinn, Kurt R.; Chaudhuri, Tandra R.; Szafran, April Adams; O’Quinn, Darrell; Weaver, Casey; Dugger, Kari; Lamar, Dale; Kesterson, Robert A.; Wang, Xiangdong; Frank, Stuart J.
2008-01-01
There has been a rapid growth of bioluminescence imaging applications in small animal models in recent years, propelled by the availability of instruments, analysis software, reagents, and creative approaches to apply the technology in molecular imaging. Advantages include the sensitivity of the technique as well as its efficiency, relatively low cost, and versatility. Bioluminescence imaging is accomplished by sensitive detection of light emitted following chemical reaction of the luciferase...
Circadian control sheds light on fungal bioluminescence.
Oliveira, Anderson G; Stevani, Cassius V; Waldenmaier, Hans E; Viviani, Vadim; Emerson, Jillian M; Loros, Jennifer J; Dunlap, Jay C
2015-03-30
Bioluminescence, the creation and emission of light by organisms, affords insight into the lives of organisms doing it. Luminous living things are widespread and access diverse mechanisms to generate and control luminescence [1-5]. Among the least studied bioluminescent organisms are phylogenetically rare fungi-only 71 species, all within the ∼ 9,000 fungi of the temperate and tropical Agaricales order-are reported from among ∼ 100,000 described fungal species [6, 7]. All require oxygen [8] and energy (NADH or NADPH) for bioluminescence and are reported to emit green light (λmax 530 nm) continuously, implying a metabolic function for bioluminescence, perhaps as a byproduct of oxidative metabolism in lignin degradation. Here, however, we report that bioluminescence from the mycelium of Neonothopanus gardneri is controlled by a temperature-compensated circadian clock, the result of cycles in content/activity of the luciferase, reductase, and luciferin that comprise the luminescent system. Because regulation implies an adaptive function for bioluminescence, a controversial question for more than two millennia [8-15], we examined interactions between luminescent fungi and insects [16]. Prosthetic acrylic resin "mushrooms," internally illuminated by a green LED emitting light similar to the bioluminescence, attract staphilinid rove beetles (coleopterans), as well as hemipterans (true bugs), dipterans (flies), and hymenopterans (wasps and ants), at numbers far greater than dark control traps. Thus, circadian control may optimize energy use for when bioluminescence is most visible, attracting insects that can in turn help in spore dispersal, thereby benefitting fungi growing under the forest canopy, where wind flow is greatly reduced. PMID:25802150
Fluorescent and Bioluminescent Reporter Myxoviruses.
Rostad, Christina A; Currier, Michael C; Moore, Martin L
2016-01-01
The advent of virus reverse genetics has enabled the incorporation of genetically encoded reporter proteins into replication-competent viruses. These reporters include fluorescent proteins which have intrinsic chromophores that absorb light and re-emit it at lower wavelengths, and bioluminescent proteins which are luciferase enzymes that react with substrates to produce visible light. The incorporation of these reporters into replication-competent viruses has revolutionized our understanding of molecular virology and aspects of viral tropism and transmission. Reporter viruses have also enabled the development of high-throughput assays to screen antiviral compounds and antibodies and to perform neutralization assays. However, there remain technical challenges with the design of replication-competent reporter viruses, and each reporter has unique advantages and disadvantages for specific applications. This review describes currently available reporters, design strategies for incorporating reporters into replication-competent paramyxoviruses and orthomyxoviruses, and the variety of applications for which these tools can be utilized both in vitro and in vivo. PMID:27527209
Fluorescent and Bioluminescent Reporter Myxoviruses
Rostad, Christina A.; Currier, Michael C.; Moore, Martin L.
2016-01-01
The advent of virus reverse genetics has enabled the incorporation of genetically encoded reporter proteins into replication-competent viruses. These reporters include fluorescent proteins which have intrinsic chromophores that absorb light and re-emit it at lower wavelengths, and bioluminescent proteins which are luciferase enzymes that react with substrates to produce visible light. The incorporation of these reporters into replication-competent viruses has revolutionized our understanding of molecular virology and aspects of viral tropism and transmission. Reporter viruses have also enabled the development of high-throughput assays to screen antiviral compounds and antibodies and to perform neutralization assays. However, there remain technical challenges with the design of replication-competent reporter viruses, and each reporter has unique advantages and disadvantages for specific applications. This review describes currently available reporters, design strategies for incorporating reporters into replication-competent paramyxoviruses and orthomyxoviruses, and the variety of applications for which these tools can be utilized both in vitro and in vivo. PMID:27527209
Bioluminescence microscopy using a short focal-length imaging lens
Ogoh, K; Akiyoshi, R.; May-Maw-Thet,; Sugiyama, T; Dosaka, S; Hatta-Ohashi, Y; Suzuki, H.
2014-01-01
Bioluminescence from cells is so dim that bioluminescence microscopy is performed using an ultra low-light imaging camera. Although the image sensor of such cameras has been greatly improved over time, such improvements have not been made commercially available for microscopes until now. Here, we customized the optical system of a microscope for bioluminescence imaging. As a result, bioluminescence images of cells could be captured with a conventional objective lens and colour imaging camera....
Bacteria bioluminescent activity as an indicator of geomagnetic disturbances
The effect of geomagnetic disturbances and storms on bioluminescence activity of bacterium were investigated. The bioluminescence intensity change depended on amplitude and continuous of geomagnetic storms. It is assumed, that the synchronization of luminous radiation take place in cellos when frequency of geomagnetic disturbances approached to an intrinsic one of a bioluminescence system. High sensitivity of bioluminescence of geomagnetic storms was detected. 5 refs., 4 figs
Nanostructured bioluminescent sensor for rapidly detecting thrombin.
Chen, Longyan; Bao, Yige; Denstedt, John; Zhang, Jin
2016-03-15
Thrombin plays a key role in thrombosis and hemostasis. The abnormal level of thrombin in body fluids may lead to different diseases, such as rheumatoid arthritis, glomerulonephritis, etc. Detection of thrombin level in blood and/or urine is one of important methods for medical diagnosis. Here, a bioluminescent sensor is developed for non-invasively and rapidly detecting thrombin in urine. The sensor is assembled through conjugating gold nanoparticles (Au NPs) and a recombinant protein containing Renilla luciferase (pRluc) by a peptide, which is thrombin specific substrate. The luciferase-catalyzed bioluminescence can be quenched by peptide-conjugating Au NPs. In the presence of thrombin, the short peptide conjugating luciferase and Au NPs is digested and cut off, which results in the recovery of bioluminescence due to the release of luciferase from Au NPs. The bioluminescence intensity at 470 nm is observed, and increases with increasing concentration of thrombin. The bioluminescence intensity of this designed sensor is significantly recovered when the thrombin digestion time lasts for 10 min. In addition, a similar linear relationship between luminescence intensity and the concentration of thrombin is found in the range of 8 nM to 8 μM in both buffer and human urine spiked samples. The limit of detection is as low as 80 pM. It is anticipated that our nanosensor could be a promising tool for clinical diagnosis of thrombin in human urine. PMID:26397418
Fluorescence and bioluminescence of bacterial luciferase intermediates
An intermediate in the luciferase-catalyzed bioluminescent oxidation of FMNH2, isolated and purified by chromatography at --200, was postulated to be an oxygenated reduced flavine-luciferase. Maintained and studied at --20 to --300, this material exhibits a relatively weak fluorescence emission peaking at about 505 nm when excited at 370 nm. It may comprise more than one species. Upon continued exposure to light at 370 nm, the intensity of this fluorescence increases, often by a factor of 5 or more, and its emission spectrum is blue shifted to a maximum at about 485 nm. Upon warming this fluorescence is lost and the fluorescence of flavine mononucleotide appears. If warming is carried out in the presence of a long chain aldehyde, bioluminescence occurs, with the appearance of a similar amount of flavine fluorescence. The bioluminescence yield is about the same with irradiated and nonirradiated samples. The bioluminescence emission spectrum corresponds exactly to the fluorescence emission spectrum of the intermediate formed by irradiation, implicating the latter as being structurally close to the emitting species in bioluminescence. (auth)
Discovery of New Substrates for LuxAB Bacterial Bioluminescence.
Jiang, Tianyu; Wang, Weishan; Wu, Xingkang; Wu, Wenxiao; Bai, Haixiu; Ma, Zhao; Shen, Yuemao; Yang, Keqian; Li, Minyong
2016-08-01
In this article, four novel substrates with long halftime have been designed and synthesized successfully for luxAB bacterial bioluminescence. After in vitro and in vivo biological evaluation, these molecules can emit obvious bioluminescence emission with known bacterial luciferase, thus indicating a new promising approach to developing the bacterial bioluminescent system. PMID:26896339
The feasibility and limits in performing tomographic bioluminescence imaging with a combined optical-PET (OPET) system were explored by simulating its image formation process. A micro-MRI based virtual mouse phantom was assigned appropriate tissue optical properties to each of its segmented internal organs at wavelengths spanning the emission spectrum of the firefly luciferase at 37 deg. C. The TOAST finite-element code was employed to simulate the diffuse transport of photons emitted from bioluminescence sources in the mouse. OPET measurements were simulated for single-point, two-point and distributed bioluminescence sources located in different organs such as the liver, the kidneys and the gut. An expectation maximization code was employed to recover the intensity and location of these simulated sources. It was found that spectrally resolved measurements were necessary in order to perform tomographic bioluminescence imaging. The true location of emission sources could be recovered if the mouse background optical properties were known a priori. The assumption of a homogeneous optical property background proved inadequate for describing photon transport in optically heterogeneous tissues and led to inaccurate source localization in the reconstructed images. The simulation results pointed out specific methodological challenges that need to be addressed before a practical implementation of OPET-based bioluminescence tomography is achieved
In vivo cell tracking with bioluminescence imaging
Molecular imaging is a fast growing biomedical research that allows the visual representation, characterization and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In vivo tracking of cells is an indispensable technology for development and optimization of cell therapy for replacement or renewal of damaged or diseased tissue using transplanted cells, often autologous cells. With outstanding advantages of bioluminescence imaging, the imaging approach is most commonly applied for in vivo monitoring of transplanted stem cells or immune cells in order to assess viability of administered cells with therapeutic efficacy in preclinical small animal models. In this review, a general overview of bioluminescence is provided and recent updates of in vivo cell tracking using the bioluminescence signal are discussed
In vivo cell tracking with bioluminescence imaging
Kim, Jung Eun; Kalimuthu, Senthilkumar; Ahn, Byeong Cheol [Dept. of Nuclear Medicine, Kyungpook National University School of Medicine and Hospital, Daegu (Korea, Republic of)
2015-03-15
Molecular imaging is a fast growing biomedical research that allows the visual representation, characterization and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In vivo tracking of cells is an indispensable technology for development and optimization of cell therapy for replacement or renewal of damaged or diseased tissue using transplanted cells, often autologous cells. With outstanding advantages of bioluminescence imaging, the imaging approach is most commonly applied for in vivo monitoring of transplanted stem cells or immune cells in order to assess viability of administered cells with therapeutic efficacy in preclinical small animal models. In this review, a general overview of bioluminescence is provided and recent updates of in vivo cell tracking using the bioluminescence signal are discussed.
Chemistry and biology of insect bioluminescence
Colepicolo Neto, P.; Bechara, E.J.H. (Sao Paulo Univ. (Brazil). Inst. de Quimica)
1984-12-01
Basic aspects on the Chemistry and Biology of bioluminescence are reviewed, with emphasis on insects. Data from the investigation of Lampyridae (fireflies) are collected from literature. With regard to Elateridae (click beetles) and Phengodidae (rail road worms), the least explored families of luminescent insects, new data are presented on the following aspects: (i) 'in vivo' emission spectra, (ii) chemical nature of the luciferin, (iii) conection between bioluminescence and 'oxygen toxicity' as a result of molecular oxygen storage and (iv) the role of light emission by larvae and pupae.
Chemistry and biology of insect bioluminescence
Basic aspects on the Chemistry and Biology of bioluminescence are reviewed, with emphasis on insects. Data from the investigation of Lampyridae (fireflies) are collected from literature. With regard to Elateridae (click beetles) and Phengodidae (rail road worms), the least explored families of luminescent insects, new data are presented on the following aspects: (i) 'in vivo' emission spectra, (ii) chemical nature of the luciferin, (iii) conection between bioluminescence and 'oxygen toxicity' as a result of molecular oxygen storage and (iv) the role of light emission by larvae and pupae. (Author)
A Multichannel Bioluminescence Determination Platform for Bioassays.
Kim, Sung-Bae; Naganawa, Ryuichi
2016-01-01
The present protocol introduces a multichannel bioluminescence determination platform allowing a high sample throughput determination of weak bioluminescence with reduced standard deviations. The platform is designed to carry a multichannel conveyer, an optical filter, and a mirror cap. The platform enables us to near-simultaneously determine ligands in multiple samples without the replacement of the sample tubes. Furthermore, the optical filters beneath the multichannel conveyer are designed to easily discriminate colors during assays. This optical system provides excellent time- and labor-efficiency to users during bioassays. PMID:27424912
Bioluminescent Bioreporters Encapsulated in Silica Gel
Kuncová, Gabriela; Trögl, J.; Demnerová, K.; Ripp, S.; Sayler, G. S.
-: -, 2008, O08-2 - 1-O08-2 - 4. [XVI International Conference on Bioencapsulation. Dublin (IE), 04.09.2008-06.09.2008] Institutional research plan: CEZ:AV0Z40720504 Keywords : bioluminescent bioreporter * silica gel * biosensor Subject RIV: CE - Biochemistry
Bioluminescence lights the way to food safety
Brovko, Lubov Y.; Griffiths, Mansel W.
2003-07-01
The food industry is increasingly adopting food safety and quality management systems that are more proactive and preventive than those used in the past which have tended to rely on end product testing and visual inspection. The regulatory agencies in many countries are promoting one such management tool, Hazard Analysis Critical Control Point (HACCP), as a way to achieve a safer food supply and as a basis for harmonization of trading standards. Verification that the process is safe must involve microbiological testing but the results need not be generated in real-time. Of all the rapid microbiological tests currently available, the only ones that come close to offering real-time results are bioluminescence-based methods. Recent developments in application of bioluminescence for food safety issues are presented in the paper. These include the use of genetically engineered microorganisms with bioluminescent and fluorescent phenotypes as a real time indicator of physiological state and survival of food-borne pathogens in food and food processing environments as well as novel bioluminescent-based methods for rapid detection of pathogens in food and environmental samples. Advantages and pitfalls of the methods are discussed.
Giachino, Vincent; Geiser, Martial
2016-01-01
Dans le cadre du projet européen BRAAVOO, qui vise à mesurer les concentrations de différents polluants présents dans la mer, nous développons un lecteur de bioluminescence embarqué dans une bouée.
Bioluminescence for determining energy state of plants
Ching, T. M.
1975-01-01
Bioluminescence produced by the luciferin-luciferase system is a very sensitive assay for ATP content in extracts of plant materials. The ATP test for seed and pollen viability and vigor is presented, along with prediction of high growth potential and productivity in new crosses and selections of breeding materials. ATP as an indicator for environmental quality, stresses, and metabolic regulation is also considered.
A Table-Based Random Sampling Simulation for Bioluminescence Tomography
Xiaomeng Zhang
2006-01-01
Full Text Available As a popular simulation of photon propagation in turbid media, the main problem of Monte Carlo (MC method is its cumbersome computation. In this work a table-based random sampling simulation (TBRS is proposed. The key idea of TBRS is to simplify multisteps of scattering to a single-step process, through randomly table querying, thus greatly reducing the computing complexity of the conventional MC algorithm and expediting the computation. The TBRS simulation is a fast algorithm of the conventional MC simulation of photon propagation. It retained the merits of flexibility and accuracy of conventional MC method and adapted well to complex geometric media and various source shapes. Both MC simulations were conducted in a homogeneous medium in our work. Also, we present a reconstructing approach to estimate the position of the fluorescent source based on the trial-and-error theory as a validation of the TBRS algorithm. Good agreement is found between the conventional MC simulation and the TBRS simulation.
Qiang Wu
2013-01-01
Full Text Available Bioluminescence tomography (BLT has a great potential to provide a powerful tool for tumor detection, monitoring tumor therapy progress, and drug development; developing new reconstruction algorithms will advance the technique to practical applications. In the paper, we propose a BLT reconstruction algorithm by combining SP3 equations and Bregman iteration method to improve the quality of reconstructed sources. The numerical results for homogeneous and heterogeneous phantoms are very encouraging and give significant improvement over the algorithms without the use of SP3 equations and Bregman iteration method.
Bioluminescent Probe for Detecting Mercury(II) in Living Mice.
Jiang, Tianyu; Ke, Bowen; Chen, Hui; Wang, Weishan; Du, Lupei; Yang, Keqian; Li, Minyong
2016-08-01
A novel bioluminescence probe for mercury(II) was obtained on the basis of the distinct deprotection reaction of dithioacetal to decanal, so as to display suitable sensitivity and selectivity toward mercury(II) over other ions with bacterial bioluminescence signal. These experimental results indicated such a probe was a novel promising method for mercury(II) bioluminescence imaging in environmental and life sciences ex vivo and in vivo. PMID:27412583
Construction of a bioluminescence reporter plasmid for Francisella tularensis
Bina, Xiaowen R.; Miller, Mark A.; James E Bina
2010-01-01
A Francisella tularensis shuttle vector that constitutively expresses the Photorhabdus luminescens lux operon in type A and type B strains of F. tularensis was constructed. The bioluminescence reporter plasmid was introduced into the live vaccine strain of F. tularensis and used to follow F. tularensis growth in a murine intranasal challenge model in real time by bioluminescence imaging. The results show that the new bioluminescence reporter plasmid represents a useful tool for tularemia rese...
Bioluminescence in the high Arctic during the polar night
Berge, Jørgen; Båtnes, Anna Solvang; Johnsen, Geir; Blackwell, Susan; Mark A. Moline
2012-01-01
This study examines the composition and activity of the planktonic community during the polar night in the high Arctic Kongsfjord, Svalbard. Our results are the first published evidence of bioluminescence among zooplankton during the Arctic polar night. The observations were collected by a bathyphotometer detecting bioluminescence, integrated into an autonomous underwater vehicle, to determine the concentration and intensity of bioluminescent flashes as a function of time of day and depth. To...
In Vivo Bioluminescence Imaging of the Murine Pathogen Citrobacter rodentium
Wiles, Siouxsie; Pickard, Karen M.; Peng, Katian; MacDonald, Thomas T.; Frankel, Gad
2006-01-01
Citrobacter rodentium is a natural mouse pathogen related to enteropathogenic and enterohemorrhagic Escherichia coli. We have previously utilized bioluminescence imaging (BLI) to determine the in vivo colonization dynamics of C. rodentium. However, due to the oxygen requirement of the bioluminescence system and the colonic localization of C. rodentium, in vivo localization studies were performed using harvested organs. Here, we report the detection of bioluminescent C. rodentium and commensal...
Reliability of a bioluminescence ATP assay for detection of bacteria.
Selan, L.; Berlutti, F; Passariello, C.; Thaller, M C; Renzini, G
1992-01-01
The reliability of bioluminescence assays which employ the luciferin-luciferase ATP-dependent reaction to evaluate bacterial counts was studied, both in vitro and on urine specimens. Bioluminescence and cultural results for the most common urinary tract pathogens were analyzed. Furthermore, the influence of the culture medium, of the assaying method, and of the phase of growth on bioluminescence readings was studied. Results show that Proteus, Providencia, and Morganella strains are not corre...
Effect of electromagnetic fields on the bacteria bioluminescent activity
The effect of electromagnetic field with frequency from 36.2 to 55.9 GHz on bioluminescence activity of bacterium were investigated. Electromagnetic field results in decrease of bioluminescence, which depends from frequency. The electromagnetic field adaptation time is higher of intrinsic time parameters of bioluminescence system. The effect has nonthermal nature. It is suggested that electromagnetic field influence connects with structure rearrangements near cell emitter. 8 refs.; 3 figs
Construction of a Bioluminescent Reporter Strain To Detect Polychlorinated Biphenyls
Layton, A C; Muccini, M.; Ghosh, M. M.; Sayler, G. S.
1998-01-01
A bioluminescent reporter strain, Ralstonia eutropha ENV307(pUTK60), was constructed for the detection of polychlorinated biphenyls by inserting the biphenyl promoter upstream of the bioluminescence genes. In the presence of a nonionic surfactant, which enhances the solubility of chlorinated biphenyls, bioluminescence was induced three- to fourfold over background by biphenyl, monochlorinated biphenyls, and Aroclor 1242. The minimum detection limits for these compounds ranged from 0.15 mg/lit...
Cloning and characterization of new bioluminescent proteins
Szent-Gyorgyi, Christopher; Ballou, Byron T.; Dagnal, Erich; Bryan, Bruce
1999-07-01
Over the past two years Prolume has undertaken a comprehensive program to clone luciferases and associated 'green fluorescent proteins' (GFPs) from marine animals that use coelenterazine as the luciferin. To data we have cloned several bioluminescent proteins, including two novel copepod luciferases and two anthozoan GFPs. These four proteins have sequences that differ greatly form previously cloned analogous proteins; the sequence diversity apparently is due to independent evolutionary origins and unusual evolutionary constraints. Thus coelenterazine-based bioluminescent systems may also manifest a variety of useful properties. We discuss form this taxonomic perspective the initial biochemical and spectral characterization of our cloned proteins. Emphasis is placed on the anthozoan luciferase-GFP systems, whose efficient resonance energy transfer has elicited much current interest.
Transformation Experiment Using Bioluminescence Genes of "Vibrio fischeri."
Slock, James
1995-01-01
Bioluminescence transformation experiments show students the excitement and power of recombinant DNA technology. This laboratory experiment utilizes two plasmids of "Vibrio fischeri" in a transformation experiment. (LZ)
Stimulated bioluminescence by fluid shear stress associated with pipe flow
Dinoflagellate can be stimulated bioluminescence by hydrodynamic agitation. Two typical dinoflagellate (Lingulodinium polyedrum and Pyrocystis noctiluca) was choosed to research stimulated bioluminescence. The bioluminescence intensity and shear stress intensity were measured using fully developed pipe flow. There is shear stress threshold to agitate organism bioluminescence. From these experiment, the response thresholds of the stimulated bioluminscence always occurred in laminar flows at a shear stress level of 0.6-3 dyn/cm2. At the same time, the spectral characteristc of dinoflagellate was recorded, the wavelength of them is about 470nm, and the full width at half maximum is approximate 30nm.
Stimulated bioluminescence by fluid shear stress associated with pipe flow
Cao Jing; Wang Jiangan; Wu Ronghua, E-mail: caojing981@126.com [Col. of Electronic Eng., Naval University of Engineering, Wuhan 430033 (China)
2011-01-01
Dinoflagellate can be stimulated bioluminescence by hydrodynamic agitation. Two typical dinoflagellate (Lingulodinium polyedrum and Pyrocystis noctiluca) was choosed to research stimulated bioluminescence. The bioluminescence intensity and shear stress intensity were measured using fully developed pipe flow. There is shear stress threshold to agitate organism bioluminescence. From these experiment, the response thresholds of the stimulated bioluminscence always occurred in laminar flows at a shear stress level of 0.6-3 dyn/cm{sup 2}. At the same time, the spectral characteristc of dinoflagellate was recorded, the wavelength of them is about 470nm, and the full width at half maximum is approximate 30nm.
Detection of ATP and NADH: A Bioluminescent Experience.
Selig, Ted C.; And Others
1984-01-01
Described is a bioluminescent assay for adenosine triphosphate (ATP) and reduced nicotineamide-adenine dinucleotide (NADH) that meets the requirements of an undergraduate biochemistry laboratory course. The 3-hour experiment provides students with experience in bioluminescence and analytical biochemistry yet requires limited instrumentation,…
Use of the liquid scintillation spectrometer in bioluminescence analysis
This review covers publications concerning analytical bioluminescence which in the main have appeared between mid-1973 and mid-1976. Outlines of some new assays and techniques are given together with modifications of existing procedures. Comments are presented on the use of the liquid scintillation spectrometer and other equipment for measuring bioluminescence. New applications are detailed and discussed
A REVIEW OF ENVIRONMENTAL APPLICATIONS OF BIOLUMINESCENCE MEASUREMENTS
This review of the recent literature on environmental applications of bioluminescence systems will focus on in vivo and in vitro bioluminescence methods that have been utilized to elucidate properties of chemicals, toxic and mutagenic effects, and to estimate biomass. The unifyin...
Tomographic bioluminescence imaging by an iteratively re-weighted minimization
Wu, Ping; Liu, Kai; Xue, Zhenwen; Guo, Wei; Qin, Chenghu; Tian, Jie
2012-03-01
Tomographic bioluminescence imaging (TBI), with visible light emission in living organisms, is an effective way of molecular imaging, which allows for the study of ongoing tumor biological processes in vivo and non-invasively. This newly developed technology enables three-dimensional accuracy localization and quantitative analysis of the target tumor cells in small animal via reconstructing the images acquired by the high-resolution imaging system. Due to the difficulty of reconstruction, which is often referred to an ill-posed inverse problem, continuous efforts are still made to find more practical and efficient approaches. In this paper, an iteratively re-weighted minimization (IRM) has been applied to reconstruct the entire source distribution, which is known as sparse signals, inside the target tissue with the limited outgoing photon density on its boundary. By introducing a weight function into the objective function, we convert the lp norm problem into a more simple form of l2 norm to reduce the computational complexity. The weight function is updated in each iterative step to compute the final optimal solution more efficiently. This method is proved to be robust to different parameters, and mouse experiments are conducted to validate the feasibility of IRM approach, which is also reliable at whole-body imaging.
Hansen, Thomas Mejer; Cordua, Knud Skou; Looms, Majken Caroline; Mosegaard, Klaus
2013-03-01
We present an application of the SIPPI Matlab toolbox, to obtain a sample from the a posteriori probability density function for the classical tomographic inversion problem. We consider a number of different forward models, linear and non-linear, such as ray based forward models that rely on the high frequency approximation of the wave-equation and 'fat' ray based forward models relying on finite frequency theory. In order to sample the a posteriori probability density function we make use of both least squares based inversion, for linear Gaussian inverse problems, and the extended Metropolis sampler, for non-linear non-Gaussian inverse problems. To illustrate the applicability of the SIPPI toolbox to a tomographic field data set we use a cross-borehole traveltime data set from Arrenæs, Denmark. Both the computer code and the data are released in the public domain using open source and open data licenses. The code has been developed to facilitate inversion of 2D and 3D travel time tomographic data using a wide range of possible a priori models and choices of forward models.
Lighting up bioluminescence with coelenterazine: strategies and applications.
Jiang, Tianyu; Du, Lupei; Li, Minyong
2016-04-13
Bioluminescence-based techniques, such as bioluminescence imaging, BRET and dual-luciferase reporter assay systems, have been widely used to examine a myriad of biological processes. Coelenterazine (CTZ), a luciferin or light-producing compound found in bioluminescent organisms, has sparked great curiosity and interest in searching for analogues with improved photochemical properties. This review summarizes the current development of coelenterazine analogues, their bioluminescence properties, and the rational design of caged coelenterazine towards biotargets, as well as their applications in bioassays. It should be emphasized that the design of caged luciferins can provide valuable insight into detailed molecular processes in organisms and will be a trend in the development of bioluminescent molecules. PMID:27009907
Dinoflagellate bioluminescence in response to mechanical stimuli in water flows
A. S. Cussatlegras
2005-01-01
Full Text Available Bioluminescence of plankton organisms induced by water movements has long been observed and is still under investigations because of its great complexity. In particular, the exact mechanism occurring at the level of the cell has not been yet fully understood. This work is devoted to the study of the bioluminescence of the dinoflagellates plankton species Pyrocystis noctiluca in response to mechanical stimuli generated by water flows. Several experiments were performed with different types of flows in a Couette shearing apparatus. All of them converge to the conclusion that stationary homogeneous laminar shear does not trigger massive bioluminescence, but that acceleration and shear are both necessary to stimulate together an intense bioluminescence response. The distribution of the experimental bioluminescence thresholds is finally calculated from the light emission response for the Pyrocystis noctiluca species.
Modulated Luminescent Tomography
Stefanov, Plamen; Cong, Wenxiang; Wang, Ge
2014-01-01
We propose and analyze a mathematical model of Modulated Luminescent Tomography. We show that when single X-rays or focused X-rays are used as an excitation, the problem is similar to the inversion of weighted X-ray transforms. In particular, we give an explicit inversion in the case of Dual Cone X-ray excitation.
Bakhsheshian, Joshua; Wei, Bih-Rong; Hall, Matthew D; Simpson, R Mark; Gottesman, Michael M
2016-01-01
We provide a detailed protocol for imaging ATP-binding cassette subfamily G member 2 (ABCG2) function at the blood-brain barrier (BBB) of transgenic mice. D-Luciferin is specifically transported by ABCG2 found on the apical side of endothelial cells at the BBB. The luciferase-luciferin enzymatic reaction produces bioluminescence, which allows a direct measurement of ABCG2 function at the BBB. Therefore bioluminescence imaging (BLI) correlates with ABCG2 function at the BBB and this can be measured by administering luciferin in a mouse model that expresses luciferase in the brain parenchyma. BLI allows for a relatively low-cost alternative for studying transporter function in vivo compared to other strategies such as positron emission tomography. This method for imaging ABCG2 function at the BBB can be used to investigate pharmacokinetic inhibition of the transporter. PMID:27424909
The incidence of missed diagnoses of acute cardiac ischemia in the emergency department could be reduced by a new imaging modality. In the present study, the clinical significance of 99mTc-pyrophosphate (PYP), 123I-β-methyl-p-iodophenyl-pentadecanoic acid (BMIPP), 201TlCl scintigraphy (imaging) and T2-weighted inversion-recovery magnetic resonance imaging (MRI) for the detection of culprit lesion in patients with acute coronary syndromes (ACS) was compared. The study group comprised 18 patients with ACS: 12 patients with acute myocardial infarction (AMI) (11 males; mean age, 63±11 years) and 6 patients with unstable angina (UA) (3 males, mean age, 67±5 years). Of the 12 patients with AMI, 10 underwent 201TlCl and PYP single photon emission computed tomography (SPECT) studies as a dual-energy acquisition (201TlCl/PYP) and 8 underwent 201TlCl SPECT within 1 week of the BMIPP study. All 18 patients underwent BMIPP SPECT and MRI. The MRI pulse sequence was black blood turbo short-inversion-time inversion recovery (STIR) (breath-hold T2-weighted studies). The T2-weighted inversion-recovery MRI showed higher sensitivity and negative predictive value than PYP and 201TlCl, and higher specificity and positive predictive value than BMIPP and 201TlCl. The area under the receiver-operating characteristic curve for PYP, BMIPP, 201TlCl and MRI was 0.787, 0.725, 0.731 and 0.878, respectively. The difference between the areas of MRI and BMIPP was significant (p<0.05). Accurate detection of culprit lesion is improved by using MRI rather than BMIPP, particularly for patients with ACS. (author)
A bioluminescent assay for measuring glucose uptake.
Valley, Michael P; Karassina, Natasha; Aoyama, Natsuyo; Carlson, Coby; Cali, James J; Vidugiriene, Jolanta
2016-07-15
Identifying activators and inhibitors of glucose uptake is critical for both diabetes management and anticancer therapy. To facilitate such studies, easy-to-use nonradioactive assays are desired. Here we describe a bioluminescent glucose uptake assay for measuring glucose transport in cells. The assay is based on the uptake of 2-deoxyglucose and the enzymatic detection of the 2-deoxyglucose-6-phosphate that accumulates. Uptake can be measured from a variety of cell types, it can be inhibited by known glucose transporter inhibitors, and the bioluminescent assay yields similar results when compared with the radioactive method. With HCT 116 cells, glucose uptake can be detected in as little as 5000 cells and remains linear up to 50,000 cells with signal-to-background values ranging from 5 to 45. The assay can be used to screen for glucose transporter inhibitors, or by multiplexing with viability readouts, changes in glucose uptake can be differentiated from overall effects on cell health. The assay also can provide a relevant end point for measuring insulin sensitivity. With adipocytes and myotubes, insulin-dependent increases in glucose uptake have been measured with 10- and 2-fold assay windows, respectively. Significant assay signals of 2-fold or more have also been measured with human induced pluripotent stem cell (iPSC)-derived cardiomyocytes and skeletal myoblasts. PMID:27130501
Development of bioluminescent Salmonella strains for use in food safety
Bailey R Hartford
2008-01-01
Full Text Available Abstract Background Salmonella can reside in healthy animals without the manifestation of any adverse effects on the carrier. If raw products of animal origin are not handled properly during processing or cooked to a proper temperature during preparation, salmonellosis can occur. In this research, we developed bioluminescent Salmonella strains that can be used for real-time monitoring of the pathogen's growth on food products. To accomplish this, twelve Salmonella strains from the broiler production continuum were transformed with the broad host range plasmid pAKlux1, and a chicken skin attachment model was developed. Results Salmonella strains carrying pAKlux1 constitutively expressed the luxCDABE operon and were therefore detectable using bioluminescence. Strains were characterized in terms of bioluminescence properties and plasmid stability. To assess the usefulness of bioluminescent Salmonella strains in food safety studies, we developed an attachment model using chicken skin. The effect of washing on attachment of Salmonella strains to chicken skin was tested using bioluminescent strains, which revealed the attachment properties of each strain. Conclusion This study demonstrated that bioluminescence is a sensitive and effective tool to detect Salmonella on food products in real-time. Bioluminescence imaging is a promising technology that can be utilized to evaluate new food safety measures for reducing Salmonella contamination on food products.
Construction of a bioluminescent reporter strain to detect polychlorinated biphenyls
Layton, A.C.; Muccini, M.; Ghosh, M.M.; Sayler, G.S. [Univ. of Tennessee, Knoxville, TN (United States)
1998-12-01
A bioluminescent reporter strain, Ralstonia eutropha ENV307 (pUTK60), was constructed for the detection of polychlorinated biphenyls by inserting the biphenyl promoter upstream of the bioluminescence genes. In the presence of a nonionic surfactant, which enhances the solubility of chlorinated biphenyls, bioluminescence was induced three- to fourfold over background by biphenyl, monochlorinated biphenyls, and Aroclor 1242. The minimum detection limits for these compounds ranged from 0.15 mg/liter for 4-chlorobiphenyl to 1.5 mg/liter for Aroclor 1242.
Razali, Azhani Mohd; Abdullah, Jaafar
2015-04-01
Single Photon Emission Computed Tomography (SPECT) is a well-known imaging technique used in medical application, and it is part of medical imaging modalities that made the diagnosis and treatment of disease possible. However, SPECT technique is not only limited to the medical sector. Many works are carried out to adapt the same concept by using high-energy photon emission to diagnose process malfunctions in critical industrial systems such as in chemical reaction engineering research laboratories, as well as in oil and gas, petrochemical and petrochemical refining industries. Motivated by vast applications of SPECT technique, this work attempts to study the application of SPECT on a Pebble Bed Reactor (PBR) using numerical phantom of pebbles inside the PBR core. From the cross-sectional images obtained from SPECT, the behavior of pebbles inside the core can be analyzed for further improvement of the PBR design. As the quality of the reconstructed image is largely dependent on the algorithm used, this work aims to compare two image reconstruction algorithms for SPECT, namely the Expectation Maximization Algorithm and the Exact Inversion Formula. The results obtained from the Exact Inversion Formula showed better image contrast and sharpness, and shorter computational time compared to the Expectation Maximization Algorithm.
Razali, Azhani Mohd, E-mail: azhani@nuclearmalaysia.gov.my; Abdullah, Jaafar, E-mail: jaafar@nuclearmalaysia.gov.my [Plant Assessment Technology (PAT) Group, Industrial Technology Division, Malaysian Nuclear Agency, Bangi, 43000 Kajang (Malaysia)
2015-04-29
Single Photon Emission Computed Tomography (SPECT) is a well-known imaging technique used in medical application, and it is part of medical imaging modalities that made the diagnosis and treatment of disease possible. However, SPECT technique is not only limited to the medical sector. Many works are carried out to adapt the same concept by using high-energy photon emission to diagnose process malfunctions in critical industrial systems such as in chemical reaction engineering research laboratories, as well as in oil and gas, petrochemical and petrochemical refining industries. Motivated by vast applications of SPECT technique, this work attempts to study the application of SPECT on a Pebble Bed Reactor (PBR) using numerical phantom of pebbles inside the PBR core. From the cross-sectional images obtained from SPECT, the behavior of pebbles inside the core can be analyzed for further improvement of the PBR design. As the quality of the reconstructed image is largely dependent on the algorithm used, this work aims to compare two image reconstruction algorithms for SPECT, namely the Expectation Maximization Algorithm and the Exact Inversion Formula. The results obtained from the Exact Inversion Formula showed better image contrast and sharpness, and shorter computational time compared to the Expectation Maximization Algorithm.
Single Photon Emission Computed Tomography (SPECT) is a well-known imaging technique used in medical application, and it is part of medical imaging modalities that made the diagnosis and treatment of disease possible. However, SPECT technique is not only limited to the medical sector. Many works are carried out to adapt the same concept by using high-energy photon emission to diagnose process malfunctions in critical industrial systems such as in chemical reaction engineering research laboratories, as well as in oil and gas, petrochemical and petrochemical refining industries. Motivated by vast applications of SPECT technique, this work attempts to study the application of SPECT on a Pebble Bed Reactor (PBR) using numerical phantom of pebbles inside the PBR core. From the cross-sectional images obtained from SPECT, the behavior of pebbles inside the core can be analyzed for further improvement of the PBR design. As the quality of the reconstructed image is largely dependent on the algorithm used, this work aims to compare two image reconstruction algorithms for SPECT, namely the Expectation Maximization Algorithm and the Exact Inversion Formula. The results obtained from the Exact Inversion Formula showed better image contrast and sharpness, and shorter computational time compared to the Expectation Maximization Algorithm
Bioluminescent determination of free fatty acids.
Kather, H; Wieland, E
1984-08-01
A simple, highly specific, and sensitive bioluminescent method for determination of free fatty acids in unextracted plasma or serum has been developed. The method is based on the activation of free fatty acids by acyl-CoA synthetase (EC 6.2.1.3). The pyrophosphate formed is used to phosphorylate fructose 6-phosphate in a reaction catalyzed by the enzyme pyrophosphate-fructose-6-phosphate phosphotransferase (EC 4.1.2.13). The triosephosphates produced from fructose 1,6-bisphosphate by aldolase are oxidized by NAD in the presence of arsenate to 3-phosphoglycerate. The NADH is detected via the bacterial NADH-linked luciferase system. Excellent agreement has been obtained by comparison with accepted methods. In addition, for the determination of serum free fatty acids, the method is particularly applicable for following lipolysis of isolated adipocytes. PMID:6486422
Bioluminescence: a versatile technique for imaging cellular and molecular features
Paley, Miranda A.
2016-01-01
Bioluminescence is a ubiquitous imaging modality for visualizing biological processes in vivo. This technique employs visible light and interfaces readily with most cell and tissue types, making it a versatile technology for preclinical studies. Here we review basic bioluminescence imaging principles, along with applications of the technology that are relevant to the medicinal chemistry community. These include noninvasive cell tracking experiments, analyses of protein function, and methods to visualize small molecule metabolites. In each section, we also discuss how bioluminescent tools have revealed insights into experimental therapies and aided drug discovery. Last, we highlight the development of new bioluminescent tools that will enable more sensitive and multi-component imaging experiments and, thus, expand our broader understanding of living systems.
Hansen, Thomas Mejer; Cordua, Knud Skou; Looms, Majken Caroline; Mosegaard, Klaus
2013-01-01
We present an application of the SIPPI Matlab toolbox, to obtain a sample from the a posteriori probability density function for the classical tomographic inversion problem. We consider a number of different forward models, linear and non-linear, such as ray based forward models that rely on the high frequency approximation of the wave-equation and ‘fat’ ray based forward models relying on finite frequency theory. In order to sample the a posteriori probability density function we make use of...
Real-Time Bioluminescence Imaging of Nitroreductase in Mouse Model.
Feng, Ping; Zhang, Huateng; Deng, Quankun; Liu, Wei; Yang, Linghui; Li, Guobo; Chen, Guo; Du, Lupei; Ke, Bowen; Li, Minyong
2016-06-01
Nitroreductase (NTR) is an endogenous reductase overexpressed in hypoxic tumors; however, its precise detection in living cells and animals remains a considerable challenge. Herein, we developed three reaction-based probes and a related bioluminescence assay for the real-time NTR detection. The high sensitivity and selectivity of probe 3, combined with its remarkable potential of bioluminescence imaging, affords a valuable approach for in vivo imaging of NTR in a tumor model mouse. PMID:27197544
Dinoflagellate bioluminescence in response to mechanical stimuli in water flows
A. S. Cussatlegras; P. Le Gal
2005-01-01
Bioluminescence of plankton organisms induced by water movements has long been observed and is still under investigations because of its great complexity. In particular, the exact mechanism occurring at the level of the cell has not been yet fully understood. This work is devoted to the study of the bioluminescence of the dinoflagellates plankton species Pyrocystis noctiluca in response to mechanical stimuli generated by water flows. Several experiments were performed with different types of ...
Dinoflagellate bioluminescence in response to mechanical stimuli in water flows
A. S. Cussatlegras; Gal, P.
2005-01-01
Bioluminescence of plankton organisms induced by water movements has long been observed and is still under investigations because of its great complexity. In particular, the exact mechanism occurring at the level of the cell has not been yet fully understood. This work is devoted to the study of the bioluminescence of the dinoflagellates plankton species Pyrocystis noctiluca in response to mechanical stimuli generated by water flows. Several experiments were performed with d...
Dinoflagellate bioluminescence in response to mechanical stimuli in water flows
Cussatlegras, A. S.; Gal, P.
2005-01-01
International audience Bioluminescence of plankton organisms induced by water movements has long been observed and is still under investigations because of its great complexity. In particular, the exact mechanism occurring at the level of the cell has not been yet fully understood. This work is devoted to the study of the bioluminescence of the dinoflagellates plankton species Pyrocystis noctiluca in response to mechanical stimuli generated by water flows. Several experiments were performe...
Shedding light on bioluminescence regulation in Vibrio fischeri
Miyashiro, Tim; Ruby, Edward G.
2012-01-01
The bioluminescence emitted by the marine bacterium Vibrio fischeri is a particularly striking result of individual microbial cells coordinating a group behavior. The genes responsible for light production are principally regulated by the LuxR-LuxI quorum-sensing system. In addition to LuxR-LuxI, numerous other genetic elements and environmental conditions control bioluminescence production. Efforts to mathematically model the LuxR-LuxI system are providing insight into the dynamics of this a...
Bioluminescence Imaging of Chlamydia muridarum Ascending Infection in Mice
Jessica Campbell; Yumeng Huang; Yuanjun Liu; Robert Schenken; Bernard Arulanandam; Guangming Zhong
2014-01-01
Chlamydial pathogenicity in the upper genital tract relies on chlamydial ascending from the lower genital tract. To monitor chlamydial ascension, we engineered a luciferase-expressing C. muridarum. In cells infected with the luciferase-expressing C. muridarum, luciferase gene expression and enzymatic activity (measured as bioluminescence intensity) correlated well along the infection course, suggesting that bioluminescence can be used for monitoring chlamydial replication. Following an intrav...
Bioluminescence-Sensing Assay for Microbial Growth Recognition
Heba Ramadan Eed; Abdel-Kader, Nora S.; Mahmoud Helmy El Tahan; Tianhong Dai; Rehab Amin
2016-01-01
The conventional methods for microbial viability quantification require cultivation and are laborious. There is consequently a widespread need for cultivation-free methods. The adenosine triphosphate (ATP) bioluminescence-sensing assay is considered an extremely effective biosensor; hence ATP is the energy currency of all living microbes and can be used as a rapid indicator of microbial viability. We developed an ATP bioluminescence-sensing assay to detect microbial viability. A biolumine...
Circadian regulation of bioluminescence in Gonyaulax involves translational control.
Morse, D.; Milos, P M; Roux, E.; Hastings, J. W.
1989-01-01
A 10-fold circadian variation in the amount of luciferin binding protein (LBP) in the marine dinoflagellate Gonyaulax polyedra is reported. This protein binds and stabilizes luciferin, the bioluminescence substrate. In early night phase, when bioluminescence is increasing and LBP levels are rising in the cell, pulse labeling experiments show that LBP is being rapidly synthesized in vivo. At other times, the rate of LBP synthesis is at least 50 times lower, while the rate of synthesis of most ...
Action of γ-radiation on bioluminescence of Noctiluca miliaris
Results of the study in the action of various doses of irradiation on the bioluminescence of Noctiluca miliaris are presented. The doses are found that stimulate the bioluminescence and the dose - effect curves are obtained. It has been shown that stimulation of Noctiluca luminescence by γ-radiation is not of a constant character and extinguishes after a period of time determined by a dose rate
Bioluminescence imaging of Chlamydia muridarum ascending infection in mice.
Jessica Campbell
Full Text Available Chlamydial pathogenicity in the upper genital tract relies on chlamydial ascending from the lower genital tract. To monitor chlamydial ascension, we engineered a luciferase-expressing C. muridarum. In cells infected with the luciferase-expressing C. muridarum, luciferase gene expression and enzymatic activity (measured as bioluminescence intensity correlated well along the infection course, suggesting that bioluminescence can be used for monitoring chlamydial replication. Following an intravaginal inoculation with the luciferase-expressing C. muridarum, 8 of 10 mice displayed bioluminescence signal in the lower with 4 also in the upper genital tracts on day 3 after infection. By day 7, all 10 mice developed bioluminescence signal in the upper genital tracts. The bioluminescence signal was maintained in the upper genital tract in 6 and 2 mice by days 14 and 21, respectively. The bioluminescence signal was no longer detectable in any of the mice by day 28. The whole body imaging approach also revealed an unexpected airway infection following the intravaginal inoculation. Although the concomitant airway infection was transient and did not significantly alter the genital tract infection time courses, caution should be taken during data interpretation. The above observations have demonstrated that C. muridarum can not only achieve rapid ascending infection in the genital tract but also cause airway infection following a genital tract inoculation. These findings have laid a foundation for further optimizing the C. muridarum intravaginal infection murine model for understanding chlamydial pathogenic mechanisms.
Interactive graphic editing tools in bioluminescent imaging simulation
Li, Hui; Tian, Jie; Luo, Jie; Wang, Ge; Cong, Wenxiang
2005-04-01
It is a challenging task to accurately describe complicated biological tissues and bioluminescent sources in bioluminescent imaging simulation. Several graphic editing tools have been developed to efficiently model each part of the bioluminescent simulation environment and to interactively correct or improve the initial models of anatomical structures or bioluminescent sources. There are two major types of graphic editing tools: non-interactive tools and interactive tools. Geometric building blocks (i.e. regular geometric graphics and superquadrics) are applied as non-interactive tools. To a certain extent, complicated anatomical structures and bioluminescent sources can be approximately modeled by combining a sufficient large number of geometric building blocks with Boolean operators. However, those models are too simple to describe the local features and fine changes in 2D/3D irregular contours. Therefore, interactive graphic editing tools have been developed to facilitate the local modifications of any initial surface model. With initial models composed of geometric building blocks, interactive spline mode is applied to conveniently perform dragging and compressing operations on 2D/3D local surface of biological tissues and bioluminescent sources inside the region/volume of interest. Several applications of the interactive graphic editing tools will be presented in this article.
Accounting for systematic errors in bioluminescence imaging to improve quantitative accuracy
Taylor, Shelley L.; Perry, Tracey A.; Styles, Iain B.; Cobbold, Mark; Dehghani, Hamid
2015-07-01
Bioluminescence imaging (BLI) is a widely used pre-clinical imaging technique, but there are a number of limitations to its quantitative accuracy. This work uses an animal model to demonstrate some significant limitations of BLI and presents processing methods and algorithms which overcome these limitations, increasing the quantitative accuracy of the technique. The position of the imaging subject and source depth are both shown to affect the measured luminescence intensity. Free Space Modelling is used to eliminate the systematic error due to the camera/subject geometry, removing the dependence of luminescence intensity on animal position. Bioluminescence tomography (BLT) is then used to provide additional information about the depth and intensity of the source. A substantial limitation in the number of sources identified using BLI is also presented. It is shown that when a given source is at a significant depth, it can appear as multiple sources when imaged using BLI, while the use of BLT recovers the true number of sources present.
Schieda, Nicola; McInnes, Matthew D.F. [The University of Ottawa, The Ottawa Hospital, Department of Medical Imaging, Ottawa, Ontario (Canada); Al-Subhi, Maali; Flood, Trevor A.; El-Khodary, Mohammed [The University of Ottawa, The Ottawa Hospital, Department of Anatomical Pathology, Ottawa, ON (Canada)
2014-11-15
Segmental enhancement inversion (SEI) is a controversial imaging finding reportedly specific for the diagnosis of renal oncocytoma. The purpose of this study was to re-evaluate SEI using biphasic CT and multiphase MRI. With research ethics board approval, a retrospective analysis of patients with resection or biopsy of oncocytoma or chromophobe renal cell carcinoma (Ch-RCC) between 2008-2012 was performed. Twenty-four patients with oncocytoma and 13 patients with Ch-RCC underwent CT, while 13 patients with oncocytoma and 10 patients with Ch-RCC underwent MRI. Two blinded radiologists reviewed the CT and MRI studies independently in separate sessions to assess for SEI. A third radiologist established consensus. Interobserver variability was calculated and diagnostic accuracy was compared using ROC and the Fisher exact test. There was no difference in detection of SEI between oncocytoma and Ch-RCC at CT [both readers (p = 0.65, 0.5) and consensus review (p = 0.29)] or MRI [both readers (p = 0.64, 0.74) and consensus review (p = 0.53)]. The interobserver variability at CT (K = 0.28-0.33) and MRI (K = 0.25-0.44) was fair. The sensitivity and specificity for diagnosis of oncocytoma were 21 % and 92 % at CT and 15 % and 90 % at MRI. SEI is not useful for the diagnosis of renal oncocytoma with CT or MRI. (orig.)
aequorine bioluminescence response to calcium in vitro and in cerebral cortex
Tricoire, Ludovic
2006-01-01
During my PhD, I investigated in vitro the calcium-dependent bioluminescence of thephotoprotein aequorin and then used its bioluminescence to image neuronal activities in theneocortical network. This genetically encoded calcium sensor can be expressed in specific cell types and its bioluminescence is not toxic and exhibit a high signal/noise ratio.I first search for mutations modifying aequorin bioluminescence, using a randommutagenesis and in vitro evolution approach. I isolated mutants show...
Marcinko, Charlotte L.J.; Martin, Adrian P.; Allen, John T.
2014-01-01
Bioluminescence within ocean surface waters is of significant interest because it can enhance the study of subsurface movement and organisms. Little is known about how bioluminescence potential (BPOT) varies spatially and temporally in the open ocean. However, light emitted from dinoflagellates often dominates the stimulated bioluminescence field. As a first step towards forecasting surface ocean bioluminescence in the open ocean, a simple ecological model is developed which simulates seasona...
Vegetable seed radiosensitivity and kinetic analysis of super-weak bioluminescence
Bioluminescence of several vegetable seeds induced by γ-rays was studied. The results show that positive relation exists between seeds bioluminescence and irradiation dose, which fits with equation Y=Y0eKD. The higher the K value is, the more intense the bioluminescence induced by γ-rays is. Significant differences among K values were found with different varieties. The bioluminescence and exterior measurement value of seed radiosensitivity showed good consistency
Bioluminescence in vivo imaging of autoimmune encephalomyelitis predicts disease
Steinman Lawrence
2008-02-01
Full Text Available Abstract Background Experimental autoimmune encephalomyelitis is a widely used animal model to understand not only multiple sclerosis but also basic principles of immunity. The disease is scored typically by observing signs of paralysis, which do not always correspond with pathological changes. Methods Experimental autoimmune encephalomyelitis was induced in transgenic mice expressing an injury responsive luciferase reporter in astrocytes (GFAP-luc. Bioluminescence in the brain and spinal cord was measured non-invasively in living mice. Mice were sacrificed at different time points to evaluate clinical and pathological changes. The correlation between bioluminescence and clinical and pathological EAE was statistically analyzed by Pearson correlation analysis. Results Bioluminescence from the brain and spinal cord correlates strongly with severity of clinical disease and a number of pathological changes in the brain in EAE. Bioluminescence at early time points also predicts severity of disease. Conclusion These results highlight the potential use of bioluminescence imaging to monitor neuroinflammation for rapid drug screening and immunological studies in EAE and suggest that similar approaches could be applied to other animal models of autoimmune and inflammatory disorders.
Rapid detection (4 h) of methicillin-resistant Staphylococcus aureus by a bioluminescence method.
Park, C. H.; Hixon, D L; McLaughlin, C M; Cook, J F
1988-01-01
A 4-h bioluminescence method for methicillin susceptibility determination was compared with reference methods. Of the Staphylococcus aureus strains tested, 80 were methicillin resistant, 180 were methicillin susceptible, and 10 were borderline susceptible. There was 100% correlation between bioluminescence and reference methods for methicillin-susceptible and methicillin-resistant strains. All borderline-susceptible strains were identified as methicillin resistant by bioluminescence.
Propensity Scores for Prediction and Characterization of Bioluminescent Proteins from Sequences
Huang, Hui-Ling
2014-01-01
Bioluminescent proteins (BLPs) are a class of proteins with various mechanisms of light emission such as bioluminescence and fluorescence from luminous organisms. While valuable for commercial and medical applications, identification of BLPs, including luciferases and fluorescent proteins (FPs), is rather challenging, owing to their high variety of protein sequences. Moreover, characterization of BLPs facilitates mutagenesis analysis to enhance bioluminescence and fluorescence. Therefore, thi...
Jiang, Tianyu; Yang, Xiaofeng; Yang, Xingye; Yuan, Mingliang; Zhang, Tianchao; Zhang, Huateng; Li, Minyong
2016-06-21
Two series of novel coelenterazine analogues (alkynes and triazoles) with imidazopyrazinone C-6 extended substitution have been designed and synthesized successfully for the extension of bioluminescent substrates. After extensive evaluation, some compounds display excellent bioluminescence properties compared with DeepBlueC in cellulo, thus becoming potential molecules for bioluminescence techniques. PMID:27197767
Daghighi, Seyedmojtaba; Sjollema, Jelmer; Harapanahalli, Akshay; Dijkstra, Rene J. B.; van der Mei, Henny C.; Busscher, Henk J.
2015-01-01
Bioluminescence imaging is used for longitudinal evaluation of bacteria in live animals. Clear relations exist between bacterial numbers and their bioluminescence. However, bioluminescence images of Staphylococcus aureus Xen29, S. aureus Xen36 and Escherichia coli Xen14 grown on tryptone soy agar in
The Expanding Toolbox of In Vivo Bioluminescent Imaging
Xu, Tingting; Close, Dan; Handagama, Winode; Marr, Enolia; Sayler, Gary; Ripp, Steven
2016-01-01
In vivo bioluminescent imaging (BLI) permits the visualization of engineered bioluminescence from living cells and tissues to provide a unique perspective toward the understanding of biological processes as they occur within the framework of an authentic in vivo environment. The toolbox of in vivo BLI includes an inventory of luciferase compounds capable of generating bioluminescent light signals along with sophisticated and powerful instrumentation designed to detect and quantify these light signals non-invasively as they emit from the living subject. The information acquired reveals the dynamics of a wide range of biological functions that play key roles in the physiological and pathological control of disease and its therapeutic management. This mini review provides an overview of the tools and applications central to the evolution of in vivo BLI as a core technology in the preclinical imaging disciplines. PMID:27446798
The Expanding Toolbox of In Vivo Bioluminescent Imaging.
Xu, Tingting; Close, Dan; Handagama, Winode; Marr, Enolia; Sayler, Gary; Ripp, Steven
2016-01-01
In vivo bioluminescent imaging (BLI) permits the visualization of engineered bioluminescence from living cells and tissues to provide a unique perspective toward the understanding of biological processes as they occur within the framework of an authentic in vivo environment. The toolbox of in vivo BLI includes an inventory of luciferase compounds capable of generating bioluminescent light signals along with sophisticated and powerful instrumentation designed to detect and quantify these light signals non-invasively as they emit from the living subject. The information acquired reveals the dynamics of a wide range of biological functions that play key roles in the physiological and pathological control of disease and its therapeutic management. This mini review provides an overview of the tools and applications central to the evolution of in vivo BLI as a core technology in the preclinical imaging disciplines. PMID:27446798
Effect of irradiation on bioluminescence spectrum of microbial ATP
The effect of irradiation on bioluminescence spectrum of dehydrated cabbage microbial ATP was studied. The results showed that the spectral bandwidth of ATP standard was from 490 to 640 nm and the peak wavelength was at 563 nm. The spectral bandwidths of irradiated dehydrated cabbage microbial ATP and CK did not change. Peak wavelengths of dehydrated cabbage irradiated at different dosages were not significantly different from that of CK. The peaks of bioluminescence spectrum of irradiated samples were higher than that of CK, which may be because of the increasing concentration of ATP, and this effect would be kept for quite a long time after irradiation. (authors)
Space application research of EMCCDs for bioluminescence imaging
Zhang, Tao
The detection of bioluminescense is widely used on the ground, while the detection of bioluminescence in space is still at the stage of detecting bright bioluminescense. With the rapid development of research in Space Life Sciences, it will be necessary to develop a detection technology to detect weak bioluminescense. Compared to other low-light detection techniques for ground, there are more advantages of EMCCDs for space application. Build a space bioluminescence imaging detection system, analysis the feasibility and capability of its will be significant. Co-Author:Xie Zongbao,Zheng Weibo
Vânia da Silva Nunes-Halldorson; Norma Letícia Duran
2003-01-01
Bioluminescent bacteria are widespread in natural environments. Over the years, many researchers have been studying the physiology, biochemistry and genetic control of bacterial bioluminescence. These discoveries have revolutionized the area of Environmental Microbiology through the use of luminescent genes as biosensors for environmental studies. This paper will review the chronology of scientific discoveries on bacterial bioluminescence and the current applications of bioluminescence in env...
Filtering and deconvolution for bioluminescence imaging of small animals
This thesis is devoted to analysis of bioluminescence images applied to the small animal. This kind of imaging modality is used in cancerology studies. Nevertheless, some problems are related to the diffusion and the absorption of the tissues of the light of internal bioluminescent sources. In addition, system noise and the cosmic rays noise are present. This influences the quality of the images and makes it difficult to analyze. The purpose of this thesis is to overcome these disturbing effects. We first have proposed an image formation model for the bioluminescence images. The processing chain is constituted by a filtering stage followed by a deconvolution stage. We have proposed a new median filter to suppress the random value impulsive noise which corrupts the acquired images; this filter represents the first block of the proposed chain. For the deconvolution stage, we have performed a comparative study of various deconvolution algorithms. It allowed us to choose a blind deconvolution algorithm initialized with the estimated point spread function of the acquisition system. At first, we have validated our global approach by comparing our obtained results with the ground truth. Through various clinical tests, we have shown that the processing chain allows a significant improvement of the spatial resolution and a better distinction of very close tumor sources, what represents considerable contribution for the users of bioluminescence images. (author)
Microtiter plate tests for segregation of bioluminescent bacteria.
Šimkus, Remigijus; Meškienė, Rita; Ledas, Žilvinas; Baronas, Romas; Meškys, Rolandas
2016-02-01
It has been recently shown that bioluminescence imaging can be usefully applied to provide new insights into bacterial self-organization. In this work we employ bioluminescence imaging to record images of nutrient rich liquid cultures of the lux-gene reporter Escherichia coli in microtiter plate wells. The images show that patterns of inhomogenous bioluminescence form along the three-phase contact lines. The paper analyzes the dependencies of the average number of luminous aggregates (clouds) on various environmental factors. In particular, our results show that optimal (neutral) pH and high aeration rates determine the highest mean number of clouds, and that spatiotemporal patterns do not form in the pH buffered suspensions. In addition, a sigmoidal (switch-like) dependence of the number of aggregates on the rate of aeration was observed. The obtained bioluminescence imaging data was interpreted by employing the Keller-Segel-Fisher (KSF) model of chemotaxis and logistic growth, adapted to systems of metabolically flexible (two-state) bacteria. The modified KSF model successfully simulated the observed switch-like responses. The results of the microtiter plate tests and their simulations indicate that the segregation of bacteria with different activities proceeds in the three-phase contact line region. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26039821
The influence of SHFEMF on bioluminescence of V. Harveyi
Exposure of bacteria V. harveyi grown on agar medium to 7 HHz electromagnetic field changes the intensity of their luminescence. It is suggested that the dynamics of the luminescence change reflects the adaptation processes in the microorganisms which accompany the electromao.netic field effect. The changes observed may be attributed to the temperature dependence of bioluminescence
Bioluminescent system for dynamic imaging of cell and animal behavior
Highlights: ► We combined a yellow variant of GFP and firefly luciferase to make ffLuc-cp156. ► ffLuc-cp156 showed improved photon yield in cultured cells and transgenic mice. ► ffLuc-cp156 enabled video-rate bioluminescence imaging of freely-moving animals. ► ffLuc-cp156 mice enabled tracking real-time drug delivery in conscious animals. -- Abstract: The current utility of bioluminescence imaging is constrained by a low photon yield that limits temporal sensitivity. Here, we describe an imaging method that uses a chemiluminescent/fluorescent protein, ffLuc-cp156, which consists of a yellow variant of Aequorea GFP and firefly luciferase. We report an improvement in photon yield by over three orders of magnitude over current bioluminescent systems. We imaged cellular movement at high resolution including neuronal growth cones and microglial cell protrusions. Transgenic ffLuc-cp156 mice enabled video-rate bioluminescence imaging of freely moving animals, which may provide a reliable assay for drug distribution in behaving animals for pre-clinical studies.
The mechanism of electronic excitation in the bacterial bioluminescent reaction
The current state of the problem of formation of the electron-excited product in the chemiluminescent reaction that underlies the bacterial luminescence is analysed. Various schemes of chemical transformations capable of producing a bacterial bioluminescence emitter are presented. The problem of excitation of secondary emitters is considered; two possible mechanisms of their excitation are analysed.
Bioluminescent system for dynamic imaging of cell and animal behavior
Hara-Miyauchi, Chikako [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Saitama 351-0198 (Japan); Department of Biophysics and Biochemistry, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo 113-8510 (Japan); Tsuji, Osahiko [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo 160-8582 (Japan); Hanyu, Aki [Division of Biochemistry, The Cancer Institute of the Japanese Foundation for Cancer Research, Tokyo 135-8550 (Japan); Okada, Seiji [Department of Advanced Medical Initiatives, Faculty of Medical Sciences, Kyushu University, Fukuoka 812-8582 (Japan); Yasuda, Akimasa [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo 160-8582 (Japan); Fukano, Takashi [Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Saitama 351-0198 (Japan); Akazawa, Chihiro [Department of Biophysics and Biochemistry, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo 113-8510 (Japan); Nakamura, Masaya [Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo 160-8582 (Japan); Imamura, Takeshi [Department of Molecular Medicine for Pathogenesis, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295 (Japan); Core Research for Evolutional Science and Technology, The Japan Science and Technology Corporation, Tokyo 135-8550 (Japan); Matsuzaki, Yumi [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Okano, Hirotaka James, E-mail: hjokano@jikei.ac.jp [Department of Physiology, Keio University School of Medicine, Tokyo 160-8582 (Japan); Division of Regenerative Medicine Jikei University School of Medicine, Tokyo 150-8461 (Japan); and others
2012-03-09
Highlights: Black-Right-Pointing-Pointer We combined a yellow variant of GFP and firefly luciferase to make ffLuc-cp156. Black-Right-Pointing-Pointer ffLuc-cp156 showed improved photon yield in cultured cells and transgenic mice. Black-Right-Pointing-Pointer ffLuc-cp156 enabled video-rate bioluminescence imaging of freely-moving animals. Black-Right-Pointing-Pointer ffLuc-cp156 mice enabled tracking real-time drug delivery in conscious animals. -- Abstract: The current utility of bioluminescence imaging is constrained by a low photon yield that limits temporal sensitivity. Here, we describe an imaging method that uses a chemiluminescent/fluorescent protein, ffLuc-cp156, which consists of a yellow variant of Aequorea GFP and firefly luciferase. We report an improvement in photon yield by over three orders of magnitude over current bioluminescent systems. We imaged cellular movement at high resolution including neuronal growth cones and microglial cell protrusions. Transgenic ffLuc-cp156 mice enabled video-rate bioluminescence imaging of freely moving animals, which may provide a reliable assay for drug distribution in behaving animals for pre-clinical studies.
Polydiacetylene Liposomal Aequorin Bioluminescent Device for Detection of Hydrophobic Compounds.
Yamamoto, Ryoko; Takegami, Shigehiko; Konishi, Atsuko; Horikawa, Hikari; Yonezawa, Sayumi; Kitade, Tatsuya
2016-06-01
In this study, a polydiacetylene liposomal aequorin bioluminescent device (PLABD) that functioned through control of the membrane transport of Ca(2+) ions was developed for detecting hydrophobic compounds. In the PLABD, aequorin was encapsulated in an internal water phase and a calcium ionophore (CI) was contained in a hydrophobic region. Membrane transport of Ca(2+) ions across the CI was suppressed by polymerization between diacetylene molecules. On addition of an analyte, the membrane transport of Ca(2+) ions across the CI increased, and Ca(2+) ions from the external water phase could diffuse into the internal water phase via the CI, which resulted in bioluminescence of the aequorin. Lidocaine, procaine, and procainamide were used as model compounds to test the validity of the detection mechanism of the PLABD. When each analyte was added to a suspension of the PLABD, bioluminescence from the aequorin in the PLABD was observed, and the level of this bioluminescence increased with increasing analyte concentration. There was a linear relationship between the logarithm of the analyte concentration and the bioluminescence for all analytes as follows: R = 0.89 from 10 nmol L(-1) to 10 mmol L(-1) for lidocaine, R = 0.66 from 10 nmol L(-1) to 100 μmol L(-1) for procaine, and R = 0.74 from 100 nmol L(-1) to 100 μmol L(-1) for procainamide. Compared to the traditional colorimetric method using polydiacetylene liposome, the PLABD was superior for both the sensitivity and dynamic range. Thus, PLABD is a valid, simple, and sensitive signal generator for detection of hydrophobic compounds that interact with PLABD membranes. PMID:27146598
2007-01-01
This media offers the student a chance to review how to exploit differential flatness of the system and emply inverse dynamics in the virtual domain to compute the states and controls that were not approximated with the reference functions. Last modified: 5/18/2009
Shah, N; Naseby, D C
2015-06-15
Whole cell biosensors have been extensively used for monitoring toxicity and contamination of various compounds and xenobiotics in environmental biology and microbial ecology; their application in the pharmaceutical and cosmetics industries has been limited. According to several pharmacopoeias, pharmaceutical products must be tested for microbial activity using traditional viable count techniques; the use of whole cell microbial biosensors potentially provides an alternative, fast, and efficient method. However there is a lack of a validated bioluminescence method. Prototype whole cell microbial biosensors have already been developed in Pseudomonas aeruginosa ATCC 9027. Validation of the bioluminescent strains was performed in accordance with the pharmacopoeia, Parenteral Drug Association and International Organisation of Standardisation. These strains demonstrated that the bioluminescent method was accurate, precise and equivalent, as compared with plate counting at a range of 10(3)-10(7) CFU/mL. Percentage recoveries using the bioluminescent method were between 70% and 130% for all bioluminescent strains and therefore the bioluminescent method was accurate according to the criteria set in PDA technical report 33. The method was also more precise (relative standard deviation less than 15%) than the traditional plate counting method or the ATP bioluminescent method. The lower limit of detection was 10(3) CFU/mL. Two-way ANOVA showed no significant difference between the traditional plate counting and the novel bioluminescent method for all bioluminescent strains. The bioluminescent constructs passed/exceeded pharmacopoeia-specified criteria for range, limit of detection, accuracy, precision and equivalence. PMID:25618377
Kandaswamy, Krishna Kumar
2011-08-17
Background: Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological application of bioluminescence has become routine and is considered essential for many medical and general technological advances. Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. So far, no specific method has been reported to identify bioluminescent proteins from primary sequence.Results: In this paper, we propose a novel predictive method that uses a Support Vector Machine (SVM) and physicochemical properties to predict bioluminescent proteins. BLProt was trained using a dataset consisting of 300 bioluminescent proteins and 300 non-bioluminescent proteins, and evaluated by an independent set of 141 bioluminescent proteins and 18202 non-bioluminescent proteins. To identify the most prominent features, we carried out feature selection with three different filter approaches, ReliefF, infogain, and mRMR. We selected five different feature subsets by decreasing the number of features, and the performance of each feature subset was evaluated.Conclusion: BLProt achieves 80% accuracy from training (5 fold cross-validations) and 80.06% accuracy from testing. The performance of BLProt was compared with BLAST and HMM. High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. 2011 Kandaswamy et al; licensee BioMed Central Ltd.
Ning, Nannan; Tian, Jie; Liu, Xia; Deng, Kexin; Wu, Ping; Wang, Bo; Wang, Kun; Ma, Xibo
2014-02-01
In mathematics, optical molecular imaging including bioluminescence tomography (BLT), fluorescence tomography (FMT) and Cerenkov luminescence tomography (CLT) are concerned with a similar inverse source problem. They all involve the reconstruction of the 3D location of a single/multiple internal luminescent/fluorescent sources based on 3D surface flux distribution. To achieve that, an accurate fusion between 2D luminescent/fluorescent images and 3D structural images that may be acquired form micro-CT, MRI or beam scanning is extremely critical. However, the absence of a universal method that can effectively convert 2D optical information into 3D makes the accurate fusion challengeable. In this study, to improve the fusion accuracy, a new fusion method for dual-modality tomography (luminescence/fluorescence and micro-CT) based on natural light surface reconstruction (NLSR) and iterated closest point (ICP) was presented. It consisted of Octree structure, exact visual hull from marching cubes and ICP. Different from conventional limited projection methods, it is 360° free-space registration, and utilizes more luminescence/fluorescence distribution information from unlimited multi-orientation 2D optical images. A mouse mimicking phantom (one XPM-2 Phantom Light Source, XENOGEN Corporation) and an in-vivo BALB/C mouse with implanted one luminescent light source were used to evaluate the performance of the new fusion method. Compared with conventional fusion methods, the average error of preset markers was improved by 0.3 and 0.2 pixels from the new method, respectively. After running the same 3D internal light source reconstruction algorithm of the BALB/C mouse, the distance error between the actual and reconstructed internal source was decreased by 0.19 mm.
Bioluminescent Ligand-Receptor Binding Assays for Protein or Peptide Hormones.
Liu, Ya-Li; Guo, Zhan-Yun
2016-01-01
Bioluminescence has been widely used in biomedical research due to its high sensitivity, low background, and broad linear range. In recent studies, we applied bioluminescence to ligand-receptor binding assays for some protein or peptide hormones based on a newly developed small monomeric Nanoluciferase (NanoLuc) reporter that has the so far brightest bioluminescence. The conventional ligand-receptor binding assays rely on radioligands that have drawbacks, such as radioactive hazards and short shelf lives. In contrast, the novel bioluminescent binding assays use the NanoLuc-based protein or peptide tracers that are safe, stable, and ultrasensitive. Thus, the novel bioluminescent ligand-receptor binding assay would be applied to more and more protein or peptide hormones for ligand-receptor interaction studies in future. In the present article, we provided detailed protocols for setting up the novel bioluminescent ligand-receptor binding assays using two representative protein hormones as examples. PMID:27424896
Marcinko, Charlotte L. J.; Martin, Adrian P.; Allen, John T.
2014-11-01
Bioluminescence within ocean surface waters is of significant interest because it can enhance the study of subsurface movement and organisms. Little is known about how bioluminescence potential (BPOT) varies spatially and temporally in the open ocean. However, light emitted from dinoflagellates often dominates the stimulated bioluminescence field. As a first step towards forecasting surface ocean bioluminescence in the open ocean, a simple ecological model is developed which simulates seasonal changes in dinoflagellate abundance. How forecasting seasonal changes in BPOT may be achieved through combining such a model with relationships derived from observations is discussed and an example is given. The study illustrates a potential new approach to forecasting BPOT through explicitly modelling the population dynamics of a prolific bioluminescent phylum. The model developed here offers a promising platform for the future operational forecasting of the broad temporal changes in bioluminescence within the North Atlantic. Such forecasting of seasonal patterns could provide valuable information for the targeting of scientific field campaigns.
Impact of Anesthesia Protocols on In Vivo Bioluminescent Bacteria Imaging Results
Chuzel, Thomas; Sanchez, Violette; Vandamme, Marc; Martin, Stéphane; Flety, Odile; Pager, Aurélie; Chabanel, Christophe; Magnier, Luc; Foskolos, Marie; Petit, Océane; Rokbi, Bachra; Chereul, Emmanuel
2015-01-01
Infectious murine models greatly benefit from optical imaging using bioluminescent bacteria to non-invasively and repeatedly follow in vivo bacterial infection. In this context, one of the most critical parameters is the bioluminescence sensitivity to reliably detect the smallest number of bacteria. Another critical point is the anesthetic approaches that have been demonstrated to impact the bioluminescence flux emission in studies with luciferase-transfected tumor cells. However, this impact...
Bioluminescence determination of active caspase-3 in single apoptotic cells
Lišková, Marcela; Klepárník, Karel; Matalová, Eva; Hegrová, Jitka; Přikryl, Jan; Švandová, Eva; Foret, František
2013-01-01
Roč. 34, č. 12 (2013), s. 1772-1777. ISSN 0173-0835 R&D Projects: GA ČR GAP206/11/2377 Grant ostatní: GA ČR(CZ) GAP502/12/1285 Institutional support: RVO:68081715 ; RVO:67985904 Keywords : apoptosis * bioluminescence * caspase-3 Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 3.161, year: 2013
Bioluminescence imaging of estrogen receptor activity during breast cancer progression.
Vantaggiato, Cristina; Dell'Omo, Giulia; Ramachandran, Balaji; Manni, Isabella; Radaelli, Enrico; Scanziani, Eugenio; Piaggio, Giulia; Maggi, Adriana; Ciana, Paolo
2016-01-01
Estrogen receptors (ER) are known to play an important regulatory role in mammary gland development as well as in its neoplastic transformation. Although several studies highlighted the contribution of ER signaling in the breast transformation, little is known about the dynamics of ER state of activity during carcinogenesis due to the lack of appropriate models for measuring the extent of receptor signaling in time, in the same animal. To this aim, we have developed a reporter mouse model for the non-invasive in vivo imaging of ER activity: the ERE-Luc reporter mouse. ERE-Luc is a transgenic mouse generated with a firefly luciferase (Luc) reporter gene driven by a minimal promoter containing an estrogen responsive element (ERE). This model allows to measure receptor signaling in longitudinal studies by bioluminescence imaging (BLI). Here, we have induced sporadic mammary cancers by treating systemically ERE-Luc reporter mice with DMBA (9,10-dimethyl 1,2-benzanthracene) and measured receptor signaling by in vivo imaging in individual animals from early stage until a clinically palpable tumor appeared in the mouse breast. We showed that DMBA administration induces an increase of bioluminescence in the whole abdominal area 6 h after treatment, the signal rapidly disappears. Several weeks later, strong bioluminescence is observed in the area corresponding to the mammary glands. In vivo and ex vivo imaging analysis demonstrated that this bioluminescent signal is localized in the breast area undergoing neoplastic transformation. We conclude that this non-invasive assay is a novel relevant tool to identify the activation of the ER signaling prior the morphological detection of the neoplastic transformation. PMID:27069764
A Novel Bioluminescent Protease Assay Using Engineered Firefly Luciferase
Wigdal, Susan S.; Anderson, Jessica L; Vidugiris, Gediminas J; Shultz, John; Wood, Keith V.; Fan, Frank
2008-01-01
Proteases play important roles in a variety of disease processes. Understanding their biological functions underpins the efforts of drug discovery. We have developed a bioluminescent protease assay using a circularly permuted form of firefly luciferase, wherein the native enzyme termini were joined by a peptide containing a protease site of interest. Protease cleavage of these mutant luciferases greatly activates the enzyme, typically over 100 fold. The mutant luciferase substrates are easily...
Bioluminescent bacteria as indicators of chemical contamination of coastal waters.
Frischer, M E; Danforth, J M; Foy, T F; Juraske, R
2005-01-01
The ratio of bioluminescent to total bacteria (bioluminescent ratio, BLR) as an indicator of a variety of types of anthropogenic contamination of estuarine ecosystems was evaluated through a series of laboratory and field studies. Laboratory studies indicated that the BLR of natural bacterioplankton communities was proportionally reduced in the presence of a number of contaminants including diesel fuel and saltmarsh sediments co-contaminated with mercury and polychlorinated biphenyls (PCBs). Bioluminescent ratio inhibition was observed after short-term exposure to a contaminant suggesting a physiological rather than a population response of native microbial communities. Simulated eutrophication did not suppress the BLR. Field observations of the BLR were conducted weekly for a 2-yr period in the Skidaway River estuary, Georgia, USA. These observations revealed considerable seasonal variability associated with the BLR. Bioluminescent ratios were highest during the summer (25 +/- 15%), lower in the fall (6 +/- 5%) and spring (3 +/- 2%), and near zero during the winter. Although the BLR was not significantly correlated to salinity at a single site (Skidaway River estuary), the BLR was significantly correlated with salinity when sites within the same estuary system were compared (r2 = 0.93). Variation in BLR was not correlated to standard bacteriological indicators of water quality including total and fecal coliform bacteria. Comparison of the BLR from impacted and pristine estuarine sites during the fall suggested that anthropogenically impacted sites exhibited lower BLR than predicted from salinity versus BLR relationships developed in pristine systems. These observations suggest that the BLR could be used as a simple and reliable initial indicator of chemical contamination of estuarine systems resulting from human activity. PMID:15998855
Detection of a bioluminescent milky sea from space
Miller, Steven D.; Haddock, Steven H. D.; Elvidge, Christopher D.; Thomas F. Lee
2005-01-01
On many occasions over the centuries, mariners have reported witnessing surreal nocturnal displays where the surface of the sea produces an intense, uniform, and sustained glow that extends to the horizon in all directions. Although such emissions cannot be fully reconciled with the known features of any light-emitting organism, these so-called “milky seas” are hypothesized to be manifestations of unusually strong bioluminescence produced by colonies of bacteria in association with a microalg...
Bioluminescence in vivo imaging of autoimmune encephalomyelitis predicts disease
Steinman Lawrence; Ho Peggy; Luo Jian; Wyss-Coray Tony
2008-01-01
Abstract Background Experimental autoimmune encephalomyelitis is a widely used animal model to understand not only multiple sclerosis but also basic principles of immunity. The disease is scored typically by observing signs of paralysis, which do not always correspond with pathological changes. Methods Experimental autoimmune encephalomyelitis was induced in transgenic mice expressing an injury responsive luciferase reporter in astrocytes (GFAP-luc). Bioluminescence in the brain and spinal co...
Bioluminescence for USP sterility testing of pharmaceutical suspension products.
Bussey, D M; K. Tsuji
1986-01-01
Bioluminescence measurement significantly improved the accuracy, sensitivity, precision, and reliability of the current visual endpoint determination for the USP sterility test and eliminated the day 7 transfer/dilution step required for testing suspension products. Thirteen strains of bacteria and fungi (representing potential contaminants in sterile products), three pharmaceutical suspension products, and four media were used in the experiment. No interference from suspension products was e...
Bacterial bioluminescence and Gumbel statistics: From quorum sensing to correlation
Delle Side, Domenico; Velardi, Luciano; Nassisi, Vincenzo; Pennetta, Cecilia; Alifano, Pietro; Talà, Adelfia; Salvatore Tredici, Maurizio
2013-12-01
We show that, in particular experimental conditions, the time course of the radiant fluxes, measured from a bioluminescent emission of a Vibrio harveyi related strain, collapse after suitable rescaling onto the Gumbel distribution of extreme value theory. We argue that the activation times of the strain luminous emission follow the universal behavior described by this statistical law, in spite of the fact that no extremal process is known to occur.
Jia, Kun; Ionescu, Rodica Elena
2016-01-01
: Bioluminescence is light production by living organisms, which can be observed in numerous marine creatures and some terrestrial invertebrates. More specifically, bacterial bioluminescence is the "cold light" produced and emitted by bacterial cells, including both wild-type luminescent and genetically engineered bacteria. Because of the lively interplay of synthetic biology, microbiology, toxicology, and biophysics, different configurations of whole-cell biosensors based on bacterial bioluminescence have been designed and are widely used in different fields, such as ecotoxicology, food toxicity, and environmental pollution. This chapter first discusses the background of the bioluminescence phenomenon in terms of optical spectrum. Platforms for bacterial bioluminescence detection using various techniques are then introduced, such as a photomultiplier tube, charge-coupled device (CCD) camera, micro-electro-mechanical systems (MEMS), and complementary metal-oxide-semiconductor (CMOS) based integrated circuit. Furthermore, some typical biochemical methods to optimize the analytical performances of bacterial bioluminescent biosensors/assays are reviewed, followed by a presentation of author's recent work concerning the improved sensitivity of a bioluminescent assay for pesticides. Finally, bacterial bioluminescence as implemented in eukaryotic cells, bioluminescent imaging, and cancer cell therapies is discussed. PMID:25981856
Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity
Widder, E. A.
2010-05-01
From bacteria to fish, a remarkable variety of marine life depends on bioluminescence (the chemical generation of light) for finding food, attracting mates, and evading predators. Disparate biochemical systems and diverse phylogenetic distribution patterns of light-emitting organisms highlight the ecological benefits of bioluminescence, with biochemical and genetic analyses providing new insights into the mechanisms of its evolution. The origins and functions of some bioluminescent systems, however, remain obscure. Here, I review recent advances in understanding bioluminescence in the ocean and highlight future research efforts that will unite molecular details with ecological and evolutionary relationships.
Extended Diffraction Tomography
Schlottmann, R B
2009-01-01
We present the development of extended diffraction tomography, a new approach to the solution of the linear seismic waveform inversion problem. This method has several appealing features, such as the use of arbitrary depth-dependent reference models and the decomposition of the full 2D or 3D inverse problem into a large number of independent 1D problems. This decomposition makes the method naturally highly parallelizable. Careful implementation yields significant robustness with respect to noise. Several synthetic examples are shown which characterize the benefits of our method and demonstrate the usefulness of choosing realistic 1D reference media.
Ando, Yoriko; Sakurai, Takashi; Koida, Kowa; Tei, Hajime; Hida, Akiko; Nakao, Kazuki; Natsume, Mistuo; Numano, Rika
2016-03-01
Bioluminescence imaging (BLI) is used in biomedical research to monitor biological processes within living organisms. Recently, fiber bundles with high transmittance and density have been developed to detect low light with high resolution. Therefore, we have developed a bundled-fiber-coupled microscope with a highly sensitive cooled-CCD camera that enables the BLI of organs within the mouse body. This is the first report of in vivo BLI of the brain and multiple organs in luciferase-reporter mice using bundled-fiber optics. With reflectance imaging, the structures of blood vessels and organs can be seen clearly with light illumination, and it allowed identification of the structural details of bioluminescence images. This technique can also be applied to clinical diagnostics in a low invasive manner. PMID:27231601