Simple cell count [I think]

Hey all, thanks for the great software, firstly.

I’m trying to do some very simple cell counts on images of Xenopus embryos injected with nuclear localised GFP mRNA - I have a succession of images in a timelapse.

That’s what they look like. But to make the process simpler, I’ll be cropping the images so that I only count cells on a portion of each embryo, because I realise the differences in luminosity would probably make things more complicated.

I’m not great with technology, but I’m certain that what I’m trying to do is a fairly simple process - simply count the green dots in each picture. Is it possible to use CellProfiler to do this, and could you please indicate how? if you could even point me towards which modes I should use, I can figure out the rest from the manual.

Thanks. :smile:


I would suggest taking a look at the Example pipelines page, where you can take your pick of pipelines to look at. You can pick one that is sufficiently close to your assay and modify it to suit your needs. Based on your brief description, the speckle counting pipeline might be worth examining. Also keep in mind that the example pipelines are exactly that: examples. They will most like require some adjustment for your images.