Calculating Percentage of an image based on color

Hey CellProfiler community,

I am working on histology images in CellProfiler and then in CellProfiler Analyst for classification purposes. Now I am looking to calculate the percentage of the image that is a certain color or falls within a certain range of colors and I would like the output of that in a percentage.

Is that task possible using this software or should I look somewhere else? I have put in a decent amount of time into CP and would like to keep using it but can’t get over this hump at the moment. The object I wish to quantify is too large and not in a uniform shape to use the primary and secondary object modulus. Any tips and tricks would be greatly appreciated!

I think you should be able to do this in 3 modules:

  • UnmixColors : to make the region you want to quantify bright on a dark background
  • Threshold: to make a binary image based on that, where your region of interest is 1 and the background is 0
  • MeasureImageIntensity: the mean intensity in the binary image will be the fraction that is 1, aka the % of a certain color
1 Like

Thank you so much Beth!