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Image filtering using anisotropic structure tensor for cell membrane enhancement in 3D microscopy

Sorin Pop, Alexandre Dufour, Jean-Christophe Olivo-Marin
2011 2011 18th IEEE International Conference on Image Processing  
More particularly in 3D microscopy, cell membranes appear as structures of co-dimension 2, and suffer from discontinuities in intensity and orientation.  ...  In this work we propose a new tensor-based anisotropic model specifically adapted to 2D planar structures able to perform noise reduction and contrast enhancement simultaneously.  ...  Fig. 4. a) Slice of a 3D microscopy image b-f) Result from different models CONCLUSION In this work we have presented a novel model for planar structures denoising and enhancement using PDE-based  ... 
doi:10.1109/icip.2011.6115880 dblp:conf/icip/PopDO11 fatcat:xynzybbsrvdyfjmz4xxqmybjaa

Multiscale tensor anisotropic filtering of fluorescence microscopy for denoising microvasculature

V. B. S. Prasath, R. Pelapur, O. V. Glinskii, V. V. Glinsky, V. H. Huxley, K. Palaniappan
2015 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)  
Fluorescence microscopy images are contaminated by noise and improving image quality without blurring vascular structures by filtering is an important step in automatic image analysis.  ...  Based on a coherency enhancing flow with planar confidence measure and fused 3D structure information, our method integrates multiple scales for microvasculature preservation and noise removal membrane  ...  We study the effects of integration of multiscale in a tensors within an anisotropic diffusion filtering framework for fluorescence microscopy images.  ... 
doi:10.1109/isbi.2015.7163930 pmid:26730456 pmcid:PMC4696606 fatcat:figs5az6cjbybcnase4vs3k56i

Anisotropic plate diffusion filtering for detection of cell membranes in 3D microscopy images

K. Mosaliganti, F. Janoos, A. Gelas, R. Noche, N. Obholzer, R. Machiraju, S. Megason
2010 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
We demonstrate the use of our methods on 3D cell membrane images of a zebrafish embryo acquired using fluorescent microscopy and quantify the improvement in image quality.  ...  We apply diffusion filtering to identify and enhance membranes.  ...  We develop an anisotropic diffusion filter for membrane images in clumped cellular regions.  ... 
doi:10.1109/isbi.2010.5490110 pmid:21766060 pmcid:PMC3136121 dblp:conf/isbi/MosaligantiJGNOMM10 fatcat:oykss2im4fdvpptpk6ntetzrle

Enhancement of cell boundaries in transmission electron microscopy images

T. Tasdizen, R. Whitaker, R. Marc, B. Jones
2005 IEEE International Conference on Image Processing 2005  
In this paper, we propose a new partial differential equation for enhancing the contrast and continuity of cell membranes in TEM images.  ...  Transmission electron microscopy (TEM) is an important modality for the analysis of cellular structures in neurobiology.  ...  In TEM images, cell membranes appear as noisy, onedimensional structures (curves), and in 3D they appear as sheets.  ... 
doi:10.1109/icip.2005.1530008 pmid:19169423 pmcid:PMC2630188 dblp:conf/icip/TasdizenWMJ05 fatcat:5qiewnc7xzcwdiht4ka4jn4dcu

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  
Results: We propose an automated framework for the segmentation of 3D microscopy images of highly cluttered environments such as developing tissues.  ...  Motivation: In developmental biology, quantitative tools to extract features from fluorescence microscopy images are becoming essential to characterize organ morphogenesis at the cellular level.  ...  Anisotropic filtering for membrane enhancement The cellular membrane can be represented by a structure of co-dimension 2, i.e. a continuous two-dimensional surface in 3D space.  ... 
doi:10.1093/bioinformatics/btt027 pmid:23337749 fatcat:lsusbdbba5epdi4csdjm23bf5q

Structure enhancement diffusion and contour extraction for electron tomography of mitochondria

Carlos Bazán, Michelle Miller, Peter Blomgren
2009 Journal of Structural Biology  
We introduce a new approach based on anisotropic nonlinear diffusion and bilateral filtering for electron tomography of mitochondria.  ...  The behavior of the combined approach is tested for visualizing the structure of a HeLa cell mitochondrion and the results we obtain are very promising.  ...  Terry Frey and the San Diego State University Mitochondria Research Group for their input and for providing the images used in our computations.  ... 
doi:10.1016/j.jsb.2009.02.009 pmid:19254765 pmcid:PMC2676713 fatcat:atnmus43ufdhbamclmzwfggrly

Semi-Automated Neuron Boundary Detection and Nonbranching Process Segmentation in Electron Microscopy Images

Elizabeth Jurrus, Shigeki Watanabe, Richard J. Giuly, Antonio R. C. Paiva, Mark H. Ellisman, Erik M. Jorgensen, Tolga Tasdizen
2012 Neuroinformatics  
The automated process first uses machine learning and image processing techniques to identify neuron membranes that deliniate the cells in each two-dimensional section.  ...  To segment nonbranching processes, the cell regions in each two-dimensional section are connected in 3D using correlation of regions between sections.  ...  Thompson, and Blake Paulin for their help in imaging the c. elegans VNC and Eric Bushong and Thomas Deerinck for their work in preparing the examples from the mouse cerebellum.  ... 
doi:10.1007/s12021-012-9149-y pmid:22644867 pmcid:PMC3914654 fatcat:vfd7t6prqjf7hapxomxw3q5v3m

Volume visualization in serial electron microscopy using local variance

David Mayerich, John C. Hart
2012 2012 IEEE Symposium on Biological Data Visualization (BioVis)  
These tensors are then used to visualize anatomical features such as cell bodies, membranes, and fibers.  ...  Local variance is also used to separate fibers (e) and cell membranes (f, h) in a single data set. Membrane color indicates surface normal.  ...  This work was funded in part by the Beckman Institute for Advanced Science and Technology.  ... 
doi:10.1109/biovis.2012.6378578 dblp:conf/biovis/MayerichH12 fatcat:xasv45h3rzc5zg4jawa5a3xugq

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  
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.  ...  However, the manual steps involved in curating thousands of putative cell segmentations have been a major bottleneck in the application of these technologies especially for cell membranes.  ...  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

VESICLE: Volumetric Evaluation of Synaptic Interfaces using Computer vision at Large Scale [article]

William Gray Roncal, Michael Pekala, Verena Kaynig-Fittkau, Dean M. Kleissas, Joshua T. Vogelstein, Hanspeter Pfister, Randal Burns, R. Jacob Vogelstein, Mark A. Chevillet, Gregory D. Hager
2015 arXiv   pre-print
Inferring brain structure from image data, such as that obtained via electron microscopy (EM), entails solving the problem of identifying biological structures in large data volumes.  ...  This paper presents VESICLE, the first known approach designed for mammalian synapse detection in anisotropic, non-post-stained data.  ...  Acknowledgements The authors thank Bobby Kasthuri, Daniel Berger, and Jeff Lichtman for providing electron microscopy data and truth labels, and Lindsey Fernandez for helpful discussions on algorithm development  ... 
arXiv:1403.3724v4 fatcat:hf5ibofj6zcz3edzdglvklby5i

Automated detection of tunneling nanotubes in 3D images

Erlend Hodneland, Arvid Lundervold, Steffen Gurke, Xue-Cheng Tai, Amin Rustom, Hans-Hermann Gerdes
2006 Cytometry Part A  
Acknowledgement I wish to thank my three supervisors for their support and encouragement during the PhD project. Their complementary background has been very useful in the process.  ...  My main supervisor, Hans-Hermann Gerdes, has always encouraged me and believed in my skills and also shown deep and honest fascination for the potential of image processing, which has been particularly  ...  The image in (A) was filtered by coherence enhancing filtering and further enhanced by ridge enhancement to obtain an image (B) well suited for automated marker generation.  ... 
doi:10.1002/cyto.a.20302 pmid:16969816 fatcat:7ut3rhpzlzhdxocllg4ildcllm

Large-Scale Automatic Reconstruction of Neuronal Processes from Electron Microscopy Images [article]

Verena Kaynig, Amelio Vazquez-Reina, Seymour Knowles-Barley, Mike Roberts, Thouis R. Jones, Narayanan Kasthuri, Eric Miller, Jeff Lichtman, Hanspeter Pfister
2013 arXiv   pre-print
The classifier output is combined with an anisotropic smoothing prior in a Conditional Random Field framework to generate multiple segmentation hypotheses per image.  ...  Automated sample preparation and electron microscopy enables acquisition of very large image data sets.  ...  Acknowledgment The authors would like to thank Daniel Berger for providing manual segmentation, and Nancy Aulet for interactively annotating the training data.  ... 
arXiv:1303.7186v1 fatcat:hcgsjcvwpndkbo242wga4czuo4

Correlative imaging of spatio-angular dynamics of molecular assemblies and cells with multimodal instant polarization microscope [article]

Ivan E. Ivanov, Li-Hao Yeh, Juan A. Perez-Bermejo, Janie R. Byrum, James Y. S. Kim, Manuel Leonetti, Shalin B. Mehta
2022 bioRxiv   pre-print
Biological function depends on the spatio-angular architecture of macromolecules - for example, functions of lipid membrane and cytoskeletal polymers arise from both the spatial and the angular organization  ...  We anticipate these developments in joint quantitative imaging of density and anisotropy to enable new studies in tissue pathology, mechanobiology, and imaging-based screens.  ...  Ivanov, and Li-Hao Yeh are co-inventors of a patent application that covers multimodal imaging system described in this manuscript. Authors have no other competing interests.  ... 
doi:10.1101/2022.02.07.479448 fatcat:yaeh42z7rbbofdp4ppur7lfutu

Cell Segmentation in 3D Confocal Images using Supervoxel Merge-Forests with CNN-based Hypothesis Selection [article]

Johannes Stegmaier, Thiago V. Spina, Alexandre X. Falcão, Andreas Bartschat, Ralf Mikut, Elliot Meyerowitz, Alexandre Cunha
2017 arXiv   pre-print
Automated segmentation approaches are crucial to quantitatively analyze large-scale 3D microscopy images.  ...  Particularly in deep tissue regions, automatic methods still fail to provide error-free segmentations.  ...  Most existing methods preprocess the images to clean and boost the signal on cell plasma membranes, e.g., using mathematical morphology [5, 7, 13] , Hessianbased edge enhancement [9, 13] or anisotropic  ... 
arXiv:1710.06608v1 fatcat:zslzouyncfhg7aq7jgh4dytlm4

Large-scale automatic reconstruction of neuronal processes from electron microscopy images

Verena Kaynig, Amelio Vazquez-Reina, Seymour Knowles-Barley, Mike Roberts, Thouis R. Jones, Narayanan Kasthuri, Eric Miller, Jeff Lichtman, Hanspeter Pfister
2015 Medical Image Analysis  
The classifier output is combined with an anisotropic smoothing prior in a Conditional Random Field framework to generate multiple segmentation hypotheses per image.  ...  Automated sample preparation and electron microscopy enables acquisition of very large image data sets.  ...  The computations in this paper were run on the Odyssey cluster supported by the FAS Science Division Research Computing Group at Harvard University.  ... 
doi:10.1016/ pmid:25791436 pmcid:PMC4406409 fatcat:bxrzur7grreulenny45vomncbi
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