Is it possible to calculate cell area/circularity once a classifier model is complete?

cellprofiler-analyst

#1

Hi,

Once a classifier model is trained and completed, I can only see the number of positive and negative cells as data in my tables. Is it possible to get the average cell circularity and cell area measurements for each image?
Thank you


#2

Hi,

I have 2 suggestions but others may have more elegant solutions:

  • The “CP way” : you can export the classification rules as a text file, then use it in CellProfiler module FilterObjects. After this module, you might need to add another MeasureObjectSizeShape to re-measure the filtered objects (explained here)

  • The “Excel/Python way” : you can use function INDEX and MATCH in Excel to find objects (tips). In this way, you may need to look for the ID of positive vs. negative objects , e.g. object number and image number, then retrieve those cells with same ID from the measurement table, and then do the desired average.

Hope it helps.