DELTR: Digital Embryo Lineage Tree Reconstructor
2011
Authors: Lou X, Kaster F, Lindner M, Kausler B, Köthe U, Höckendorf B, Wittbrodt J, Jänicke H, Hamprecht FA
CellNetworks People: Hamprecht Fred, Wittbrodt Joachim
Journal: ISBI 2011 Proceedings, 1557-1560 [10.1109/ISBI.2011.5872698]

We present DELTR, an automated pipeline for the analysis of time-resolved light sheet fluorescence microscopy images of zebrafish embryogenesis. It comprises 3D nucleus segmen- tation using shape-regularized graph cuts, parallelized extrac- tion of geometrical features, and cell tracking by means of combinatorial optimization. We also discuss the interactive visualization software used for validating the results, and de- scribe our advances towards reconstructing the entire cell lin- eage tree of the zebrafish. Our method achieves ca. 96 % accuracy for cell nucleus detection and ca. 90 % accuracy for the association of nuclei across subsequent time steps.