Counting the number of Nuclei/cell and nuclear density in IHC image


I am very new to Cellprofiler and I am attempting to count the number of nuclei/cell in my IHC image. I have converted the image to gray using the ColorToGrayModule, and then inverted the image using ImageMath.

I am attempting to identify the nuclei as my primary object, and cell border as my secondary object. The goal is to count the amount of DNA/cell (density) and number nuclei/cell. Is there a module that already does something like this?


UnmixColors is typically more helpful for IHC images- see this blog post for some examples.

In order to count nuclei per cell though, you’ll need to be able to pretty accurately define cell boundaries between cells- that’s often tricky on tissue images. You may want to use the ilastik approach defined in that post to better define the boundaries to make this more doable.

Good luck!