I am trying to use Cell Profiler to count the number of cells in an image from a Calcein stain and am using the IdentifyPrimaryObjects module to do so. However, the program is unable to distinguish between a few cells packed closely together, which is fairly common in these images, and is thus returning an incorrect count.
I have tried altering the “Method to distinguish clumped obejcts” and “Method to draw lines between clumped objects” to almost every combination. Intensity for both seems to work best, but still does not separate between close groups.
How can I make this counting process more accurate? Is there another module I should use?
Thank you in advance for any help!