Software for determining confluency of epithelial cells


This is an image of epithelial cells at 20x.

Analysis goals

I would like to quantitatively determine the confluency in this image. Ideally I’d like to use something that can analyze many images automatically and output the confluency measurements to a table or excel.


  • What stops you from proceeding?
    Unsure how to use parameters in PHANTAST. Unfamiliar with CellProfiler and unsure if it’s suitable for analyzing phase contrast images.

  • What have you tried already?
    I’ve tried using PHANTAST, which is a segmentation plugin. It doesn’t seem to provide an accurate estimate and I’m not sure whether that has to do with my picture quality or with optimizing the parameters sigma and epsilon.

  • What software packages and/or plugins have you tried?
    PHANTAST. I’m also curious if CellProfiler would be better and if so where I can find a basic tutorial for using CellProfiler for my specific use-case.

Here is the image of my cells that goes along with the above post!