CellProfiler Worm Pipeline Usage on Xenopus Embryos


I was curious if anyone was using the CellProfiler Worm Pipeline that identifies and measures the worm’s dimensions? I saw online that it uses OilRed staining and that’s how the software identifies the worms.

Is the use of fluorescence required by CellProfiler to identify the worm? I was wanting to try it out on Xenopus embryos (around Stage 24-26) to help me quantify phenotype. I guess I could possibly micro-inject a fluorescent dextrans if the software requires it and could recognize it…

Has anyone used CellProfiler to image and measure Xenopus embryos?


For brightfield images worm pipeline needs to be modified. Add thresholding module to convert into binary images and then use IdentifyPrimaryObject module to detect them. This will work and hopefully you don’t need to add fluorescent stains.