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Image filtering using anisotropic structure tensor for cell membrane enhancement in 3D microscopy
2011
2011 18th IEEE International Conference on Image Processing
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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
2015
2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)
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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
2010
2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro
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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
2005
IEEE International Conference on Image Processing 2005
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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
2013
Computer applications in the biosciences : CABIOS
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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
2009
Journal of Structural Biology
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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
2012
Neuroinformatics
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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
2012
2012 IEEE Symposium on Biological Data Visualization (BioVis)
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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
2012
PLoS Computational Biology
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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]
2015
arXiv
pre-print
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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
2006
Cytometry Part A
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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]
2013
arXiv
pre-print
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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]
2022
bioRxiv
pre-print
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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]
2017
arXiv
pre-print
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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
2015
Medical Image Analysis
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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/j.media.2015.02.001
pmid:25791436
pmcid:PMC4406409
fatcat:bxrzur7grreulenny45vomncbi
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