ArticleBiological imaging2024
Topology-based segmentation of 3D confocal images of emerging hematopoietic stem cells in the zebrafish embryo.
Article in Biological imaging, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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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.
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