pipeline for fast semantic segmentation of microscopy images of 3D cell cultures

de Jong MA, Adegeest E, Bérenger-Currias NMLP, Mircea M, Merks RMH, et al. (2024) The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion. PLOS Computational Biology 20(2): e1011825. https://doi.org/10.1371/journal.pcbi.1011825

Here, we publish all scripts to reproduce the analyses in the manuscript Sciphy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data