Cells as primary objects rather than secondary objects


I’m working with mesenchymal cells images are all phase contrast gray color. When I try to identify objects (using the pipeline attached) in nc image compared to 141-1 (attached), it gives very small secondary objects that are much more than the number of cells and since I do not have control over the size of secondary objects , I would like to know if I can skip the "identify secondary objects " option and treat cells as primary objects. This way I can set the size within a range that includes cells and I get much better results, any thoughts?
eccentricity-area shape.cpproj (98.2 KB)


I will point you to our FAQ item on this subject. However, after playing around with your images with a bit I’m not sure whether CellProfiler is up to the task, short of using a florescent stain of some kind.


And to your question about using only IdentifyPrimaryObjects and not Secondary – yes, you can certainly do that, and remove the IDSecondary. But I agree with Mark, in that adding a simple DAPI (or whatever) marker, if at all possible, would be the most robust solution.