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Structure Tensor Based Analysis of Cells and Nuclei Organization in Tissues

Wenxing Zhang, Jerome Fehrenbach, Annaick Desmaison, Valerie Lobjois, Bernard Ducommun, Pierre Weiss
2016 IEEE Transactions on Medical Imaging  
We address the problem of automatically analyzing spatial organization of cells or nuclei in 2D or 3D images of tissues.  ...  We propose an original theoretical analysis of this tool and show that it allows quantifying two important features of nuclei in tissues: their privileged orientation as well as the ratio between the length  ...  D. is recipient of a doctoral fellowship from the Association pour la Recherche contre le Cancer and is as student of the école de l'INSERM Liliane Bettencourt.  ... 
doi:10.1109/tmi.2015.2470093 pmid:26292339 fatcat:wyufrij2ybbdth557lbpqx47o4

An Automatic Segmentation Approach of Epithelial Cells Nuclei [chapter]

Claudia Mazo, Maria Trujillo, Liliana Salazar
2012 Lecture Notes in Computer Science  
Histology images are used to identify biological structures present in living organisms -cells, tissues, organs, and parts of organs.  ...  The structure of cells varies according to the type and function of the cell. Automatic cell segmentation is one of the challenging tasks in histology image processing.  ...  Introduction Tissue samples are used to study biological structures present in living organisms. The samples contain information about cells and their distribution.  ... 
doi:10.1007/978-3-642-33275-3_70 fatcat:6so5qp3kpfb5zdl2oruw4fmjjm

Quantitative metric profiles capture three-dimensional temporospatial architecture to discriminate cellular functional states

Lindsey McKeen-Polizzotti, Kira M Henderson, Basak Oztan, C Cagatay Bilgin, Bülent Yener, George E Plopper
2011 BMC Medical Imaging  
Cell-graphs were proposed to characterize the spatial organization between the cells in tissues by exploiting graph theory wherein the nuclei of the cells constitute the nodes and the approximate adjacency  ...  Computational analysis of tissue structure reveals sub-visual differences in tissue functional states by extracting quantitative signature features that establish a diagnostic profile.  ...  Acknowledgements This work was partially supported by National Institutes of Health Grant #RO1 EB008016.  ... 
doi:10.1186/1471-2342-11-11 pmid:21599975 pmcid:PMC3125246 fatcat:pgdm267ze5ajfivtlepw4txtcq

Extracting 3D cell parameters from dense tissue environments: application to the development of the mouse heart

Sorin Pop, Alexandre C. Dufour, Jean-François Le Garrec, Chiara V. Ragni, Clémire Cimper, Sigolène M. Meilhac, Jean-Christophe Olivo-Marin
2013 Computer applications in the biosciences : CABIOS  
The approach is based on a partial differential equation framework that jointly takes advantage of the nuclear and cellular membrane information to enable accurate extraction of nuclei and cells in dense  ...  However, automated image analysis in this context is a challenging task, owing to perturbations induced by the acquisition process, especially in organisms where the tissue is dense and opaque.  ...  Hence, systematic analysis of developing tissues composed of several thousands of cells calls for robust and automated tools to segment cells, nuclei and other subcellular structures from 3D fluorescence  ... 
doi:10.1093/bioinformatics/btt027 pmid:23337749 fatcat:lsusbdbba5epdi4csdjm23bf5q

Identifying Loose Connective and Muscle Tissues on Histology Images [chapter]

Claudia Mazo, Maria Trujillo, Liliana Salazar
2013 Lecture Notes in Computer Science  
Histology images are used to identify biological structures present in living organisms -cells, tissues, and organs -correctly.  ...  The structure of tissues varies according to the type and purpose of the tissue. Automatic identification of tissues is an open problem in image processing.  ...  The structure tensor of an image is a method of analysing the edge structure in an image.  ... 
doi:10.1007/978-3-642-41827-3_22 fatcat:agondjxgbfc77jdqykx63plykm

Multiscale Feature Analysis of Salivary Gland Branching Morphogenesis

Cemal Cagatay Bilgin, Shayoni Ray, Banu Baydil, William P. Daley, Melinda Larsen, Bülent Yener, Johannes Jaeger
2012 PLoS ONE  
Multiscale cell-graph analysis was most effective in classification of the tissue state.  ...  Whereas tensor analysis demonstrate that epithelial tissue was affected the most by inhibition of ROCK signaling, significant multiscale changes in mesenchymal tissue organization were identified with  ...  Acknowledgments The authors thank George Plopper, Sharon Sequeira, and Basak Oztan for useful discussions. Author Contributions  ... 
doi:10.1371/journal.pone.0032906 pmid:22403724 pmcid:PMC3293912 fatcat:vpgsaubocbcrrfv5fqtybw6s6q

Multiscale Characterization of Engineered Cardiac Tissue Architecture

Nancy K. Drew, Nicholas E. Johnsen, Jason Q. Core, Anna Grosberg
2016 Journal of Biomechanical Engineering  
The engineered cells and tissues were stained for four architectural structures: actin, tubulin, sarcomeric z-lines, and nuclei.  ...  In this work, we utilize a variety of architecture metrics to quantify organization and consistency of single structures over multiple scales, from subcellular to tissue scale as well as correlation of  ...  Robinson, Tuyetnhi Le, Marlen Tagle Rodriguez, and Priyanka Ganesh for participating in gathering single cell data used in this work. We are indebted to Professor Susan Rafelski and Dr.  ... 
doi:10.1115/1.4034656 pmid:27617880 pmcid:PMC6993780 fatcat:krsoyyomsvhr7dfwqmksp6h3i4

Coupled Analysis of In Vitro and Histology Tissue Samples to Quantify Structure-Function Relationship

Evrim Acar, George E. Plopper, Bülent Yener, Helmut Ahammer
2012 PLoS ONE  
We also show that our techniques can differentiate between the structural organization of native tissues and their corresponding in vitro engineered cell culture models.  ...  Features are calculated from graph theoretical representations of tissue structures and the data are analyzed in the form of matrices and higher-order tensors using matrix and tensor factorization methods  ...  One fundamental characteristic of both diseases is tissue failure: namely, errors in the structural organization and function of cells in the affected tissues.  ... 
doi:10.1371/journal.pone.0032227 pmid:22479315 pmcid:PMC3316529 fatcat:ypwcdbyu4rcqxh5rmqyzgwo67a

The link between diffusion MRI and tumor heterogeneity: Mapping cell eccentricity and density by diffusional variance decomposition (DIVIDE)

Filip Szczepankiewicz, Danielle van Westen, Elisabet Englund, Carl-Fredrik Westin, Freddy Ståhlberg, Jimmy Lätt, Pia C. Sundgren, Markus Nilsson
2016 NeuroImage  
Quantitative microscopy was performed on the excised tumor tissue, where structural anisotropy and cell density were quantified by structure tensor analysis and cell nuclei segmentation, respectively.  ...  The structural heterogeneity of tumor tissue can be probed by diffusion MRI (dMRI) in terms of the variance of apparent diffusivities within a voxel.  ...  All authors contributed to the writing of the manuscript. Funding information  ... 
doi:10.1016/j.neuroimage.2016.07.038 pmid:27450666 pmcid:PMC5159287 fatcat:qm3tk6nsjza7dfjpt2bwd2mpm4

Identifying nuclear phenotypes using semi-supervised metric learning

Shantanu Singh, Firdaus Janoos, Thierry Pécot, Enrico Caserta, Gustavo Leone, Jens Rittscher, Raghu Machiraju
2011 Information processing in medical imaging : proceedings of the ... conference  
In systems-based approaches for studying processes such as cancer and development, identifying and characterizing individual cells within a tissue is the first step towards understanding the large-scale  ...  Results are presented on images of tumor stroma in breast cancer, where the framework is used to identify fibroblasts, macrophages and endothelial cells--three major stromal cells involved in carcinogenesis  ...  Acknowledgments This work was supported by National Institutes of Health Grants UL1RR025755 and 5 P01 CA 097189-05.  ... 
pmid:21761673 pmcid:PMC4285701 fatcat:3khj2xcqmrgqdboqekhjpua6jm

Probing mouse brain microstructure using oscillating gradient diffusion MRI

Manisha Aggarwal, Melina V. Jones, Peter A. Calabresi, Susumu Mori, Jiangyang Zhang
2011 Magnetic Resonance in Medicine  
The OGSE tensor images demonstrated frequency-dependent changes in diffusion measurements, including apparent diffusion coefficient (ADC) and fractional anisotropy (FA), in major brain structures.  ...  Maps of the rate of change in ADC with oscillating gradient frequency revealed novel tissue contrast in the mouse hippocampus, cerebellum, and cerebral cortex.  ...  The nuclei of the granule cells in the GrDG have an average diameter of 5.66 μm (39) , and the diameters of the nuclei of the pyramidal cells in the hippocampus are approximately 6.5 -7.4 μm (40).  ... 
doi:10.1002/mrm.22981 pmid:21590726 pmcid:PMC3162097 fatcat:jjvyo3ietzcqxbnhxydcprdvjq

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes

Kishore R. Mosaliganti, Ramil R. Noche, Fengzhu Xiong, Ian A. Swinburne, Sean G. Megason, Robert F. Murphy
2012 PLoS Computational Biology  
The quantification of cell shape, cell migration, and cell rearrangements is important for addressing classical questions in developmental biology such as patterning and tissue morphogenesis.  ...  We present a novel and fully automated method to first reconstruct membrane signals and then segment out cells from 3D membrane images even in dense tissues.  ...  Acknowledgments We thank members of Megason lab for comments and support, Mr. Dante D'India for fish care, and Dr. Arnaud Gelas, Mr. Nicolas Rannou, and Ms.  ... 
doi:10.1371/journal.pcbi.1002780 pmid:23236265 pmcid:PMC3516542 fatcat:5dlgcotfsbewfovda7ikcyavwu

Epithelial Area Detection in Cytokeratin Microscopic Images Using MSER Segmentation in an Anisotropic Pyramid [chapter]

Cristian Smochina, Radu Rogojanu, Vasile Manta, Walter Kropatsch
2011 Lecture Notes in Computer Science  
The objective of semantic segmentation in microscopic images is to extract the cellular, nuclear or tissue components.  ...  The crypts separation and lumen detection is performed by imposing topological constraints about the epithelial layer distribution within the tissue and the round-like shape of the crypt.  ...  This coherence-enhancing filtering uses the structure tensor of the initial image (in our case the result of the histogram equalization) and a diffusion tensor D.  ... 
doi:10.1007/978-3-642-24855-9_28 fatcat:prt3x4qjcba5ff5bynrbqdoa4y

Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Yifu Ding, Daniel J Vanselow, Maksim A Yakovlev, Spencer R Katz, Alex Y Lin, Darin P Clark, Phillip Vargas, Xuying Xin, Jean E Copper, Victor A Canfield, Khai C Ang, Yuxin Wang (+5 others)
2019 eLife  
Shape and volume were computed for populations of nuclei such as those of motor neurons and red blood cells.  ...  Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective.  ...  We thank Steven Peckins and Drs. Timothy Cooper and Gordon Kindlemann for critical insight in the early stages of the project's conception and development.  ... 
doi:10.7554/elife.44898 pmid:31063133 pmcid:PMC6559789 fatcat:vsh3h2wpujcvnkng2vlrurlku4

Liquid-crystal organization of liver tissue

Hernán Morales-Navarrete, Hidenori Nonaka, Andre Scholich, Fabián Segovia-Miranda, Walter de Back, Kirstin Meyer, Roman L Bogorad, Victor Koteliansky, Lutz Brusch, Yannis Kalaidzidis, Frank Jülicher, Benjamin M Friedrich (+1 others)
2019 eLife  
In the liver, a structural model of the lobule was pioneered by Elias in 1949. This model, however, is in contrast with the apparent random 3D arrangement of hepatocytes.  ...  Surprisingly, analysis of the spatial organization of cell polarity revealed that hepatocytes are not randomly oriented but follow a long-range liquid-crystal order.  ...  We acknowledge generous allocation of computer time by the Center for Information Services and High Performance Computing (ZIH) at TU Dresden.  ... 
doi:10.7554/elife.44860 pmid:31204997 pmcid:PMC6598764 fatcat:q3vw2hk4q5adjkle72clq55ude
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