Cell counting - is it possible to get data on cell area?

Hi guys,

I have been playing around with Ilastik as a new method to quantify my cells and its working a lot better for me than previous methods. I was just wondering if there was a way to be able to get more data from the cells than just density - for example area per cell, total area of cells per ROI etc.

Has anyone been able to do so? Or can recommend a pipeline that has similar accuracy to Ilastiks?

All the best :slight_smile:

Hi @nicole1,

first of all, great that ilastik has proven useful for you.
it sounds like you are using the density counting workflow. I’m afraid that in this workflow there is no real concept of a “cell” as an object. It estimates the density at any given point and then integrates over this estimate.

If, by any chance, your cells are not heavily overlapping, touching, or you have an additional marker that could help with the segmentation (dapi?) I’d suggest to use a combination of doing Pixel Classification and object classification. Because there you get a lot of measurements per object that you can then do any statistics/visualization with. But this depends on the data you’re using, of course.