Computational protocol: Characterization of the bHLH family of transcriptional regulators in the acoel S. roscoffensis and their putative role in neurogenesis

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Protocol publication

[…] Given the difficulty of staging the embryos in the laboratory, we relied, as a good approximation for developmental time, on the number of cells. Embryo cell counting was performed by incubation of all samples for 10 min with Dapi. A sample of 12 individuals from a pool of 12–24 h’ post-fertilization embryos were scanned completely using a Leica SP2 confocal laser microscope and their stacks were processed using the software Fiji [] with the plugin “cell counter” (author: Kurt de Vos; see This procedure allowed us to obtain a precise count of the total number of cells per embryo when performing in situ procedures. […]

Pipeline specifications

Software tools Cell Counter, ImageJ
Application Microscopic phenotype analysis
Organisms Symsagittifera roscoffensis, Xenoturbella bocki, Caenorhabditis elegans