I’m new to Cell Profiler, but am hoping to set up a pipeline to measure cell area of cardiac cells in heart tissue using wheat germ agglutinin stain (WGA). I’ve been able to manipulate some of the filters to remove background within the cells, but the objects that IdentifyPrimAutomatic is defining as objects are not what I’m seeing as outlined cells on the slide. Is there a way to manipulate the automated process since I’m hoping to use it to measure a large number of slides and would like to avoid manually outlining the cells myself?
Also, if I can solve that problem, I’d like to set up a second filter to remove cells/obejcts that are not of a specific dimension (like in longitudinal section when I’d like to measure cross section) before making the measurements. Is this possible, and can you recommend a module to work with for this?
Thanks so much!