I have put together a pipeline that counts cells in an image and counts the number of green fluorescent punctae as well. I am currently having issues getting CellProfiler to accurately count the number of cells in each image. I first use the “EnhanceorSuppressFeatures” before I apply the “IdentifyPrimaryObjects” and where it says “feature size” I entered 150 (my largest cell is roughly about 150 pixels in diameter). I have used 80 in the past and that seemed to have worked a little bit better however the “?” help button does say “enter the diameter of the largest speckle” so I’m a little bit confused on how I could optimize this value.
CellCounter.cpproj (79.6 KB)
Please let me know if you think I should be using a different thresholding method. I thought Robust would work better but Imnot sure if it’s the best one for counting cells. Thank you so much in advance!
This is what I currently get, There should about 44 cells in this image. Thank you