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Authors: Emmanuel Soubies 1 ; Pierre Weiss 1 and Xavier Descombes 2

Affiliations: 1 Université de Toulouse and CNRS, France ; 2 MORPHEME team, France

ISBN: 978-989-8565-41-9

Keyword(s): Nuclei Segmentation, 2D and 3D Images, Graph-cuts, Marked Point Processes, Ellipses and Ellipsoids, Multiple Object Detection, Multiple Birth and Cut, Bio-imaging.

Related Ontology Subjects/Areas/Topics: Applications ; Bayesian Models ; Computer Vision, Visualization and Computer Graphics ; Feature Selection and Extraction ; Image Understanding ; Medical Imaging ; Object Recognition ; Pattern Recognition ; Shape Representation ; Software Engineering ; Stochastic Methods ; Theory and Methods

Abstract: We propose some improvements of the Multiple Birth and Cut algorithm (MBC) in order to extract nuclei in 2D and 3D images. This algorithm based on marked point processes was proposed recently in (Gamal Eldin et al., 2012). We introduce a new contrast invariant energy that is robust to degradations encountered in fluorescence microscopy (e.g. local radiometry attenuations). Another contribution of this paper is a fast algorithm to determine whether two ellipses (2D) or ellipsoids (3D) intersect. Finally, we propose a new heuristic that strongly improves the convergence rates. The algorithm alternates between two birth steps. The first one consists in generating objects uniformly at random and the second one consists in perturbing the current configuration locally. Performance of this modified birth step is evaluated and examples on various image types show the wide applicability of the method in the field of bio-imaging.

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Paper citation in several formats:
Soubies, E.; Weiss, P. and Descombes, X. (2013). A 3D Segmentation Algorithm for Ellipsoidal Shapes - Application to Nuclei Extraction.In Proceedings of the 2nd International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM, ISBN 978-989-8565-41-9, pages 97-105. DOI: 10.5220/0004308100970105

@conference{icpram13,
author={Emmanuel Soubies. and Pierre Weiss. and Xavier Descombes.},
title={A 3D Segmentation Algorithm for Ellipsoidal Shapes - Application to Nuclei Extraction},
booktitle={Proceedings of the 2nd International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM,},
year={2013},
pages={97-105},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004308100970105},
isbn={978-989-8565-41-9},
}

TY - CONF

JO - Proceedings of the 2nd International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM,
TI - A 3D Segmentation Algorithm for Ellipsoidal Shapes - Application to Nuclei Extraction
SN - 978-989-8565-41-9
AU - Soubies, E.
AU - Weiss, P.
AU - Descombes, X.
PY - 2013
SP - 97
EP - 105
DO - 10.5220/0004308100970105

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