I am a new learner of the CellProfiler. I want to distinguish the red and green fluorescence seeds from a batch of photos. Now I have trouble with the fluorescence intensity thresholds setting. Problems may happen in the IdentifyPrimaryObject module and FliterObjects module setting. I wonder how to set a fluorescence threshold like these pictures. Is there any module output a list of fluorescence intensity? Or is there any similar pipeline? Sincerely ask for helps:pray:
Have you tried the DisplayHistogram module? If you have measured cell intensity using MeasureObjectIntensity, then you should be able to pick the measurement of interest in DisplayHistogram near the end of the pipeline. That will let you choose a threshold based on your data.
Thank you, Carpenter. I have tried the DisplayHistogram module. It seems that the module displays the histogram individually for a group of pictures. Actually, I want to draw a picture that displays the cumulative count for multi-group of pictures. So how can I use it properly? Sincerely ask for help:pray:
Ah, then I’m pretty sure your best bet is to use
- Export to Spreadsheet, then make a histogram in Google sheets or Excel.
- Use CellProfiler Analyst which has all kinds of plotting tools.
I think 1 is easiest for your case.
Thanks, Carpenter! It works:grinning: Thanks a lot.