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A 3D Segmentation Algorithm for Ellipsoidal Shapes - Application to Nuclei Extraction

2013 Proceedings of the 2nd International Conference on Pattern Recognition Applications and Methods   unpublished
We propose some improvements of the Multiple Birth and Cut algorithm (MBC) in order to extract nuclei in 2D and 3D images.  ...  Another contribution of this paper is a fast algorithm to determine whether two ellipses (2D) or ellipsoids (3D) intersect.  ...  The authors wish to thank F. Malgouyres and J. Fehrenbach for interesting discussions. They also thank Valérie Lobjois, Charlotte Emery, Jacques  ... 
doi:10.5220/0004308100970105 fatcat:mrau63se4fgstc6pxqf6f5vvpm

Efficient, interactive, and three-dimensional segmentation of cell nuclei in thick tissue sections

Stephen J. Lockett, Damir Sudar, Curtis T. Thompson, Dan Pinkel, Joe W. Gray
1998 Cytometry  
Because automatic algorithms do not correctly segment all nuclei in tissue sections, interactive algorithms may be preferable for some applications.  ...  Existing interactive segmentation algorithms require the analyst to draw a border around the nucleus under consideration in all successive two-dimensional (2D) planes of the 3D image.  ...  Therefore a single, 6-connected 3D binary erosion was applied to the segmented objects. This application made FN Ͼ FP for some objects and FP Ͼ FN for others.  ... 
doi:10.1002/(sici)1097-0320(19980401)31:4<275::aid-cyto7>;2-i pmid:9551603 fatcat:hjspnxy2eraydk3oclhqxsrzwm

Graph Cut Based Segmentation of Predefined Shapes: Applications to Biological Imaging [chapter]

Emmanuel Soubies, Pierre Weiss, Xavier Descombes
2014 Advances in Intelligent Systems and Computing  
We propose an algorithm to segment 2D ellipses or 3D ellipsoids. This problem is of fundamental importance in various applications of cell biology.  ...  The algorithm consists of minimizing a contrast invariant energy defined on sets of non overlapping ellipsoids.  ...  Vieu for providing images and interesting discussions regarding micro pillars detection. They thank all the ITAV staff for their warm welcome in a biology laboratory.  ... 
doi:10.1007/978-3-319-12610-4_10 fatcat:ueeh4zmi7zezli74dh5sun2leq

A generic classification-based method for segmentation of nuclei in 3D images of early embryos

Jaza Gul-Mohammed, Ignacio Arganda-Carreras, Philippe Andrey, Vincent Galy, Thomas Boudier
2014 BMC Bioinformatics  
Results: We present a new automatic algorithm to segment and simultaneously classify cell nuclei in 3D/4D images.  ...  No merging of nuclei was found. Conclusion: We developed a novel generic algorithm for segmentation and classification in 3D images.  ...  Acknowledgements The authors thank the different people for providing 3D/4D datasets so we could test and improve our algorithm.  ... 
doi:10.1186/1471-2105-15-9 pmid:24423252 pmcid:PMC3900670 fatcat:y5r7pkxijrgojdyix2llyxqvma

3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells

Tong Luo, Huan Chen, Ghassan S. Kassab, Thomas Abraham
2016 PLoS ONE  
This paper introduces a new 3D segmentation algorithm to determine VSMC morphology and orientation. Fig 4. a) An idealized shape model of single cell was showed.  ...  Blue indicates the nucleus, and green indicates the cell. b) A different slice at z = 9μm was analyzed to depict various layers of contours. c) 3D rendering of cells and nuclei from a representative sample  ...  An efficient segmentation algorithm is needed to improve accuracy of 3D reconstruction for a single cell.  ... 
doi:10.1371/journal.pone.0147272 pmid:26882342 pmcid:PMC4755581 fatcat:huo7i5xpsnhctpwtxirwlvjepy

Reconstruction of Cellular Biological Structures from Optical Microscopy Data

K. Mosaliganti, L. Cooper, R. Sharp, R. Machiraju, G. Leone, Kun Huang, J. Saltz
2008 IEEE Transactions on Visualization and Computer Graphics  
The work reported here demonstrates that a suitable methodology can be conceived which isolates modality-dependent effects from the larger segmentation task and that 3D reconstructions can be cognizant  ...  Later, another segmentation effort based on a variant of Voronoi tessellations improves the delineation of the cell boundaries using a Bayesian formulation.  ...  ACKNOWLEDGEMENTS We gratefully thank the researchers providing images for this study: Jian Chen, Weiming Xia (Center for Neurologic Disease, Brigham and Women's Hospital, Harvard Medical School, Clonogenic  ... 
doi:10.1109/tvcg.2008.30 pmid:18467760 fatcat:22bkiwxvvvdijepxnnqg7xf3bm

Tumor Cell Load and Heterogeneity Estimation From Diffusion-Weighted MRI Calibrated With Histological Data: an Example From Lung Cancer

Yi Yin, Oliver Sedlaczek, Benedikt Muller, Arne Warth, Margarita Gonzalez-Vallinas, Bernd Lahrmann, Niels Grabe, Hans-Ulrich Kauczor, Kai Breuhahn, Irene E. Vignon-Clementel, Dirk Drasdo
2018 IEEE Transactions on Medical Imaging  
Color deconvolution followed by cell nuclei segmentation was performed on digitized histological images to determine local and cell-type specific 2d (two-dimensional) densities. From these the 3d  ...  Diffusion-weighted magnetic resonance imaging (DWI) is a key non-invasive imaging technique for cancer diagnosis and tumor treatment assessment, reflecting Brownian movement of water molecules in tissues  ...  ACKNOWLEDGMENT We thank Johannes Lotz and Janine Olesch for providing us with the registered images ( [38] ). We also thank the reviewers for their useful comments.  ... 
doi:10.1109/tmi.2017.2698525 pmid:28463188 fatcat:dspd2rifpvhlhgjsrpc6cuyxby

Ellipsoid Segmentation Model for Analyzing Light-Attenuated 3D Confocal Image Stacks of Fluorescent Multi-Cellular Spheroids

Michaël Barbier, Steffen Jaensch, Frans Cornelissen, Suzana Vidic, Kjersti Gjerde, Ronald de Hoogt, Ralph Graeser, Emmanuel Gustin, Yolanda T. Chong, Thomas Abraham
2016 PLoS ONE  
The spheroids are assumed to be approximately ellipsoid in shape.  ...  And quantitative analysis of large 3D image data sets is challenging, creating a need for methods which can be applied to large-scale experiments and account for impeding factors.  ...  Spheroid-masks with low 2D circularity do not have a 2D ellipse shape, and will not give rise to a satisfying 3D ellipsoid fit.  ... 
doi:10.1371/journal.pone.0156942 pmid:27303813 pmcid:PMC4909318 fatcat:2tcwxyc4cnhc7pwmlbalforpxq

A Rapid and Efficient 2D/3D Nuclear Segmentation Method for Analysis of Early Mouse Embryo and Stem Cell Image Data

Xinghua Lou, Minjung Kang, Panagiotis Xenopoulos, Silvia Muñoz-Descalzo, Anna-Katerina Hadjantonakis
2014 Stem Cell Reports  
To address this need, we developed MINS (modular interactive nuclear segmentation) as a MATLAB/ C++-based segmentation tool tailored for counting cells and fluorescent intensity measurements of 2D and  ...  An extensive evaluation of MINS on both 2D and 3D images, and comparison to related tools, reveals improvements in segmentation accuracy and usability.  ...  Schrode for providing data for analysis and J. Mackenzie, N. Saiz, and N. Schrode for feedback on the software and comments on the manuscript.  ... 
doi:10.1016/j.stemcr.2014.01.010 pmid:24672759 pmcid:PMC3964288 fatcat:yw3zptwitrgv7owxjmtv77bmqq

Shaped 3D Singular Spectrum Analysis for Quantifying Gene Expression, with Application to the Early Zebrafish Embryo

Alex Shlemov, Nina Golyandina, David Holloway, Alexander Spirov
2015 BioMed Research International  
The method includes depth equalization on the sphere, flattening, interpolation to a regular grid, pattern extraction by Shaped 3D singular spectrum analysis (SSA), and interpolation back to original nuclear  ...  Here, we present a new approach for studying gene expression in nuclei located in a thick layer around a spherical surface.  ...  NIH Grant R01-GM072022, and The Russian Foundation for Basic Research Grants 13-04-02137 and 15-04-06480.  ... 
doi:10.1155/2015/986436 pmid:26495320 pmcid:PMC4606214 fatcat:6yck6xratfa3jpmngrakir3lbm

3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification

Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Syed S. Husain, Jeffrey R. de Wett, Gerald A. Higgins, Gen Zheng, Amy Creekmore, John W. Wiley (+6 others)
2018 Scientific Reports  
To our knowledge, this is the first attempt to combine these methods for 3D nuclear shape modeling and morphometry into a highly parallel pipeline workflow for morphometric analysis of thousands of nuclei  ...  Thus, there is a compelling need for robust 3D nuclear morphometric techniques to carry out population-wide analysis.  ...  We also would like to thank colleagues at the Laboratory of Neuro Imaging (LONI), at the Keck School of Medicine, University of Southern California, for providing technical support for the LONI Pipeline  ... 
doi:10.1038/s41598-018-31924-2 pmid:30209281 pmcid:PMC6135819 fatcat:kqrmkyfhdvffzcskzkjwenve5q

Chromosome territories have a highly nonspherical morphology and nonrandom positioning

A. Khalil, J. L. Grant, L. B. Caddle, E. Atzema, K. D. Mills, A. Arneodo
2007 Chromosome Research  
This prompted us to develop a novel approach, based on the two-dimensional (2D) wavelet-transform modulus maxima (WTMM) method, adapted to perform objective and rigorous CT segmentation from nuclear background  ...  One reason for this has been the difficulty in imaging, segmenting, and analyzing structures with variable or imprecise boundaries.  ...  Kestener for technical assistance and C. Moskalenko, A. Pombo, J. Bewersdorff, and L. Shopland for interesting discussions. A. Khalil and J. Grant acknowledge A.K.  ... 
doi:10.1007/s10577-007-1172-8 pmid:17926137 fatcat:jjz744ghdjbfrjn4zlyyzhrzke

Segmentation of confocal microscope images of cell nuclei in thick tissue sections

1999 Journal of Microscopy  
The approach first uses automatic algorithms to separate the 3D image into regions of fluorescence-stained nuclei and unstained background.  ...  Segmentation of intact cell nuclei from three-dimensional (3D) images of thick tissue sections is an important basic capability necessary for many biological research studies.  ...  and Dr Jason Lieb for providing the C. elegans embryos, testing the segmentation software and for his suggestions that helped us improve the visualization program (daVinci  ... 
doi:10.1046/j.1365-2818.1999.00463.x pmid:10199001 fatcat:ddkygtcxw5hh3mxv4kfgfrdmqy

3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification [article]

Alexandr A. Kalinin, Ari Allyn-Feuer, Alex Ade, Gordon-Victor Fon, Walter Meixner, David Dilworth, Syed S. Husain, Jeffrey R. de Wet, Gerald A. Higgins, Gen Zheng, Amy Creekmore, John W. Wiley (+6 others)
2018 bioRxiv   pre-print
To our knowledge, this is the first attempt to combine these methods for 3D nuclear shape modeling and morphometry into a highly parallel pipeline workflow for morphometric analysis of thousands of nuclei  ...  Thus, there is a compelling need for robust 3D nuclear morphometric techniques to carry out population-wide analysis.  ...  These properties allow application of this algorithm to any shape, including, for example, crescent-shaped, multi-lobed, and folded, as long as shape topology is homeomorphic to a sphere.  ... 
doi:10.1101/313411 fatcat:hrifz7az2vcivfeg4trwnsimpu

Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks

Johannes Stegmaier, Jens C. Otte, Andrei Kobitski, Andreas Bartschat, Ariel Garcia, G. Ulrich Nienhaus, Uwe Strähle, Ralf Mikut, Konradin Metze
2014 PLoS ONE  
Most available algorithms that provide sufficient segmentation quality, however, are infeasible for a large amount of data due to their high complexity.  ...  In this contribution we present a fast parallelized segmentation method that is especially suited for the extraction of stained nuclei from microscopy images, e.g., of developing zebrafish embryos.  ...  GAC failed to nicely extract the shape of the nuclei due to poor edge information and GFT tended to produce segments that were too large.  ... 
doi:10.1371/journal.pone.0090036 pmid:24587204 pmcid:PMC3937404 fatcat:5hunpa7k6vc5jgbjthn2x5pesm
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