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© The Author(s), 2024. Published by Cambridge University Press. This work is licensed under the Creative Commons Attribution License This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited. (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

We develop a novel method for image segmentation of 3D confocal microscopy images of emerging hematopoietic stem cells. The method is based on the theory of persistent homology and uses an optimal threshold to select the most persistent cycles in the persistence diagram. This enables the segmentation of the image’s most contrasted and representative shapes. Coupling this segmentation method with a meshing algorithm, we define a pipeline for 3D reconstruction of confocal volumes. Compared to related methods, this approach improves shape segmentation, is more ergonomic to automatize, and has fewer parameters. We apply it to the segmentation of membranes, at subcellular resolution, of cells involved in the endothelial-to-hematopoietic transition (EHT) in the zebrafish embryos.

Details

Title
Topology-based segmentation of 3D confocal images of emerging hematopoietic stem cells in the zebrafish embryo
Author
Nardi, G 1   VIAFID ORCID Logo  ; Torcq, L 2 ; Schmidt, A A 3 ; Olivo-Marin, J-C 1 

 Biological Image Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France; CNRS UMR3691, Paris, France 
 Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France; CNRS UMR3738, Paris, France; Collège doctoral, Sorbonne Université, Paris, France 
 Department of Developmental and Stem Cell Biology, Institut Pasteur, Université Paris Cité, Paris, France; CNRS UMR3738, Paris, France 
Publication year
2024
Publication date
Nov 2024
Publisher
Cambridge University Press
e-ISSN
2633903X
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
3126619809
Copyright
© The Author(s), 2024. Published by Cambridge University Press. This work is licensed under the Creative Commons Attribution License This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited. (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.