Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Book Sections Year : 2011

Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging

Abstract

The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and μm spatial resolution.

Dates and versions

hal-00723346 , version 1 (09-08-2012)

Identifiers

Cite

Miguel Angel Luengo-Oroz, Thierry Savy, José L. Rubio-Guivernau, Louise Duloquin, Emmanuel Faure, et al.. Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging. Biomedical Imaging : From Nano to Macro, IEEE Institute of Electrical and Electronics Engineers, pp.1561-1564, 2011, IEEE International Symposium on Biomedical Imaging, 978-1-4244-4127-3. ⟨10.1109/ISBI.2011.5872699⟩. ⟨hal-00723346⟩
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