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Factor Analysis of Dynamic Sequence with Spatial Prior for 2D Cardiac Spect Sequences Analysis [chapter]

Marc Filippi, Michel Desvignes, Eric Moisan, Catherine Ghezzi, Pascale Perret, Daniel Fagret
2016 Lecture Notes in Computer Science  
Future works include tests on larger database and quantitative analysis of the robustness.  ...  This prior can be automatically defined because the method is robust to the location and shape of the prior. Tests on synthetic and SPECT dataset show the efficiency and the potential of this method.  ...  Then, to obtain the pure time-activity curve (TAC) of each organ, methods based on region of interest (ROI) give poor results.  ... 
doi:10.1007/978-3-319-48680-2_21 fatcat:jnwdfi3xqjh3bbk7p5gbox57yy

Temporal Unmixing of Dynamic Fluorescent Images by Blind Source Separation Method with a Convex Framework

Duofang Chen, Jimin Liang, Kui Guo
2015 Computational and Mathematical Methods in Medicine  
By recording a time series of tomographic images, dynamic fluorescence molecular tomography (FMT) allows exploring perfusion, biodistribution, and pharmacokinetics of labeled substances in vivo.  ...  Several numerical simulations and phantom experiments are conducted to investigate the performance of the proposed temporal unmixing method.  ...  In [15] , PCA is used to detect and visualize changes in kinetic behaviors between different regions from 3D dynamic FMT images. In [16] , Liu et al.  ... 
doi:10.1155/2015/713424 pmid:26089974 pmcid:PMC4458298 fatcat:5v5slga2rrayxa3jxaiojsnpqu

Constrained Inversion and Spectral Unmixing in Multispectral Optoacoustic Tomography

Lu Ding, Xose Luis Dean-Ben, Neal C. Burton, Robert W. Sobol, Vasilis Ntziachristos, Daniel Razansky
2017 IEEE Transactions on Medical Imaging  
Furthermore, imposing the non-negativity constraint directly on the unmixed distribution of the probe of interest was found to maintain the most robust and accurate reconstruction performance in all experiments  ...  Accurate extraction of physical and biochemical parameters from optoacoustic images is often impeded due to the use of unrigorous inversion schemes, incomplete tomographic detection coverage, or other  ...  Furthermore, imposing the non-negativity constraint directly on the unmixed distribution of the probe of interest was found to maintain the most robust and accurate reconstruction performance in all experiments  ... 
doi:10.1109/tmi.2017.2686006 pmid:28333622 pmcid:PMC5585740 fatcat:mbplye4ssfevverkxggchodjf4

Efficient 3-D Model-Based Reconstruction Scheme for Arbitrary Optoacoustic Acquisition Geometries

Lu Ding, Xose Luis Dean-Ben, Daniel Razansky
2017 IEEE Transactions on Medical Imaging  
Furthermore, imposing the non-negativity constraint directly on the unmixed distribution of the probe of interest was found to maintain the most robust and accurate reconstruction performance in all experiments  ...  Accurate extraction of physical and biochemical parameters from optoacoustic images is often impeded due to the use of unrigorous inversion schemes, incomplete tomographic detection coverage or other experimental  ...  Furthermore, imposing the non-negativity constraint directly on the unmixed distribution of the probe of interest was found to maintain the most robust and accurate reconstruction performance in all experiments  ... 
doi:10.1109/tmi.2017.2704019 pmid:28504935 fatcat:6i7sqsdb4bf27lmejm3apotocq

Highly multiplexed imaging of biosensors in live cells [article]

Jr-Ming Yang, Wei-Yu Chi, Jessica Liang, Pablo A Iglesias, Chuan-Hsiang Huang
2020 bioRxiv   pre-print
Mixed populations of barcoded cells expressing different biosensors can be concurrently imaged and computationally unmixed to achieve highly multiplexed tracking of biochemical activities in live cells  ...  We overcome this problem by developing a set of barcoding proteins that are spectrally separable from commonly used FRET (fluorescence resonance energy transfer)-based and single-fluorophore biosensors  ...  In general, the robustness of linear unmixing reduces with increasing numbers of component fluorophores.  ... 
doi:10.1101/2020.12.11.419655 fatcat:wfbczyaoxbfhnbdlrxifkxldmq

Imaging Mycobacterium tuberculosis in Mice with Reporter Enzyme Fluorescence

Riti Sharan, Hee-Jeong Yang, Preeti Sule, Jeffrey D. Cirillo
2018 Journal of Visualized Experiments  
Reporter enzyme fluorescence (REF) utilizes substrates that are specific for enzymes present in target organisms of interest for imaging or detection by fluorescence or bioluminescence.  ...  We describe the imaging of M. tuberculosis infection using a FRET substrate with maximal emission at 800 nm. The wavelength of the substrate allows sensitive deep tissue imaging in mammals.  ...  For fluorescence quantification, go to Region of Interest (ROI) Tools, add ROI cube to the organ of interest and adjust cube size to cover the organ of interest. Click on measure 3D ROIs. 13.  ... 
doi:10.3791/56801 pmid:29553533 pmcid:PMC5931367 fatcat:jqs4a7eku5b7vicckrdpy65ubm

Blind source unmixing in multi-spectral optoacoustic tomography

Jürgen Glatz, Nikolaos C. Deliolanis, Andreas Buehler, Daniel Razansky, Vasilis Ntziachristos
2011 Optics Express  
The method can further identify tissue biomarkers by decomposing the spectral contributions of different photo-absorbing molecules of interest.  ...  In this work we investigate the performance of blind source unmixing methods and spectral fitting approaches in decomposing the contributions of fluorescent dyes from the tissue background, based on MSOT  ...  Additionally, the use of blind unmixing was successfully demonstrated in the time domain by separation of blood veins based on dynamic changes of an optoacoustic image sequence.  ... 
doi:10.1364/oe.19.003175 pmid:21369139 fatcat:dneicbqo7fg4tgzr2lycdeczkq

Assessing 16S marker gene survey data analysis methods using mixtures of human stool sample DNA extracts [article]

Nathan D Olson, M. Senthil Kumar, Shan Li, Stephanie Hao, Winston Timp, Marc L Salit, O. Colin Stine, Hector Corrada Bravo
2018 bioRxiv   pre-print
The abundance of Mothur and QIIME features specific to unmixed samples and titrations were explained by sampling alone.  ...  However, for DADA2 over a third of the unmixed sample and titration specific feature abundance could not be explained by sampling alone.  ...  Official contribution of NIST; not subject to copyrights in USA. Author details  ... 
doi:10.1101/400226 fatcat:an33ujrmhrddvl3sjeabwl2q2m

Dynamical Spectral Unmixing of Multitemporal Hyperspectral Images

Simon Henrot, Jocelyn Chanussot, Christian Jutten
2016 IEEE Transactions on Image Processing  
In this paper, we consider the problem of unmixing a time series of hyperspectral images. We propose a dynamical model based on linear mixing processes at each time instant.  ...  The spectral signatures and fractional abundances of the pure materials in the scene are seen as latent variables, and assumed to follow a general dynamical structure.  ...  First, we design an abundance map for the first frame composed of three overlapping circular regions.  ... 
doi:10.1109/tip.2016.2562562 pmid:27164590 fatcat:xwjss2vs7ffqpotujc5w3t6ony

A temporally constrained ICA (TCICA) technique for artery-vein separation of cerebral microvasculature

Hatef Mehrabian, Liis Lindvere, Bojana Stefanovic, Anne L. Martel, Robert C. Molthen, John B. Weaver
2010 Medical Imaging 2010: Biomedical Applications in Molecular, Structural, and Functional Imaging  
This technique is also fully automatic and does not require specifying regions of interest which is critical in model based techniques.  ...  A dynamic data set of 50 images taken by a two-photon laser scanning microscopy technique that monitors the passage of a bolus of dye through artery and vein is used here.  ...  The authors would like to thank the Natural Sciences and Engineering Research Council of Canada (NSERC) for supporting this work.  ... 
doi:10.1117/12.844913 fatcat:oq3aqfiyv5eathzghrmwafff4a

Modern Trends in Imaging X: Spectral Imaging in Preclinical Research and Clinical Pathology

Richard Levenson, Joseph Beechem, George McNamara
2012 Analytical Cellular Pathology  
This chapter will present an overview of the rationale for spectral imaging, and discuss the hardware, software and sample labeling strategies that can optimize its usefulness in clinical settings.  ...  Spectral imaging methods are attracting increased interest from researchers and practitioners in basic science, pre-clinical and clinical arenas.  ...  Using these spectra, the image was unmixed (although classification would have given the same results) to delineate RNA-rich regions of the nucleus.  ... 
doi:10.1155/2012/904828 pmid:22475632 pmcid:PMC4605801 fatcat:5ktr6lizlje6voujowl4hummqu

All-phase MR Angiography Using Independent Component Analysis of Dynamic Contrast Enhanced MRI Time Series: .PHI.-MRA

Kiyotaka SUZUKI, Hitoshi MATSUZAWA, Hironaka IGARASHI, Masaki WATANABE, Naoki NAKAYAMA, Ingrid L. KWEE, Tsutomu NAKADA
2003 Magnetic Resonance in Medical Sciences  
Dynamic contrast enhanced magnetic resonance imaging (dynamic MRI) represents a MRI version of non-diŠusible tracer methods, the main clinical use of which is the physiological construction of what is  ...  Accordingly, we applied ICA to dynamic MRI time series. The technique was found to be powerful, allowing for hitherto unobtainable assessment of regional cerebral hemodynamics in vivo.  ...  The study was supported by grants from the Ministry of Education, Culture, Sports, Science, and Technology (Japan) and Department of Veterans AŠair Research Service.  ... 
doi:10.2463/mrms.2.23 pmid:16210816 fatcat:kprdxkvvtzgz5dqs6656uoz5b4

Robust unmixing of tumor states in array comparative genomic hybridization data

David Tolliver, Charalampos Tsourakakis, Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
2010 Computer applications in the biosciences : CABIOS  
The method builds on the prior geometric approach but uses a novel objective function allowing for robust fits that greatly reduces the sensitivity to noise and outliers.  ...  Motivation: Tumorigenesis is an evolutionary process by which tumor cells acquire sequences of mutations leading to increased growth, invasiveness, and eventually metastasis.  ...  ) the relative effect of noise on hard versus robust unmixing.  ... 
doi:10.1093/bioinformatics/btq213 pmid:20529894 pmcid:PMC2881397 fatcat:3drhfqdt6rb7fi34bqjupioev4

dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues [article]

Kristen R Maynard, Madhavi Tippani, Yoichiro Takahashi, BaDoi N Phan, Thomas M Hyde, Andrew E Jaffe, Keri Martinowich
2019 bioRxiv   pre-print
We first demonstrate robustness of our platform in single mouse neurons by quantifying differential expression of activity-regulated genes.  ...  We then quantify spatial gene expression in human dorsolateral prefrontal cortex (DLPFC) using spectral imaging and dotdotdot to mask lipofuscin autofluorescence.  ...  ACKNOWLEDGEMENTS We are grateful for the contributions of the Clinical Brain Disorders Branch of the National Institute of Mental Health in assisting the Lieber Institute for Brain Development in the acquisition  ... 
doi:10.1101/781559 fatcat:yjrocjbq3zfpldlvq4kpkdfe54

CLASI-FISH: Principles of combinatorial labeling and spectral imaging

Alex M. Valm, Jessica L. Mark Welch, Gary G. Borisy
2012 Systematic and Applied Microbiology  
The CLASI technique involves labeling microbes of interest with combinations of probes coupled with spectral imaging to allow the use of fluorophores with highly overlapping excitation and emission spectra  ...  Although the number of phylotypes present in a microbial community may number in the hundreds or more, until recently, fluorescence in situ hybridization has been used to label, at most, only a handful  ...  Synthesize two, or more, different oligonucleotide sequences specific for labeling a particular organism in the context of its community. Each probe sequence targets a different part of the 16S rRNA.  ... 
doi:10.1016/j.syapm.2012.03.004 pmid:22521573 pmcid:PMC3407316 fatcat:7ax6gdgjfbaunm7occbveo6ez4
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