I’ve been setting up a pipeline in CellProfiler to count cellular organelles (peroxisomes). The method used to stain the peroxisomes (viral infection with GFP labeled peroxisome localization tag) is such that signal intensity can be uneven between cells (in some cells, all the peroxisomes have a strong staining pattern while in others they have a weak pattern).
This means that a pipeline based on signal intensities of the organelles is difficult to use, it will either overestimate or underestimate the number in part of the population.
As mentioned in the original post (from 9 years ago!), ImageJ has a function called “Find Maxima” that I find extremely robust for identifying and counting objects like this, even if signal intensities vary greatly. However, ImageJ does not lend itself to analyzing many images, identifying cells, etc.
The module that mbray mentions above no longer seems to be a part of CellProfiler. Is there any other function that would give the same results?