I just started using CellProfiler the other day and still have some problems figuring out the right settings. I did a basic Hoechst staining and wanna count the number of nuclei as well as the average nuclei size. I have two main problems:
the nuclei size on my pictures are ranging from 15µm to 80µm and I haven’t figured out a way yet I can count them both, without either getting multiple counts for the big nuclei or only 1 count for multiple small nuclei. I used several setting including discarding objects outside of range, changing nuclei diameter etc…
I have a big heterogeneity in my staining intensities meaning some of the nuclei are really bright others are rather dark. The dark ones are not getting counted.
Is there any way I can set the cell profiler to include all of the nuclei.
Thanks for your help.
I attached a sample picture