Hello, I am new to Cellprofiler and ImageJ and also don’t have a solid software development background so my question may sound dumb. Sorry.
I have a segmentation task for the immunohistochemical images containing reaction for KI-67, HER2, etc.
I want to create a simple code snippet able to load an image (or just read it from a hardcoded path), perform segmentation (to distinguish “positive” and “negative” cells) and output total, positive and negative counts.
Is it something Cellprofiler and/or ImageJ capable to do? Can you please suggest related Classes and Methods do yo it? Or, maybe it is already some CLI / Python Notebook version I can use?
I guess I can use UI to do this but I need a code snippet to allow batch processing.
Please see attached images w/ example of the input file and manually (it took like forever!) segmented cells: