TY - GEN
T1 - Processing pipeline for digitalizing the lineage tree of early zebrafish embryogenesis from multiharmonic imaging
AU - Luengo-Oroz, Miguel A.
AU - Savy, Thierry
AU - Rubio, Jose L.
AU - Duloquin, Louise
AU - Faure, Emmanuel
AU - Olivier, Nicolas
AU - Ledesma-Carbayo, Maria
AU - Debarre, Delphine
AU - Bourgine, Paul
AU - Beaurepaire, Emmanuel
AU - Peyrieras, Nadine
AU - Santos, Andres
PY - 2011/1/1
Y1 - 2011/1/1
N2 - 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 m spatial resolution [1].
AB - 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 m spatial resolution [1].
KW - in-vivo imaging
KW - lineage tree
KW - multiphoton microscopy
KW - viscous watershed
KW - zebrafish development
U2 - 10.1109/ISBI.2011.5872699
DO - 10.1109/ISBI.2011.5872699
M3 - Conference contribution
AN - SCOPUS:80055042010
SN - 9781424441280
T3 - Proceedings - International Symposium on Biomedical Imaging
SP - 1561
EP - 1564
BT - 2011 8th IEEE International Symposium on Biomedical Imaging
PB - IEEE Computer Society
T2 - 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2011
Y2 - 30 March 2011 through 2 April 2011
ER -