If you want to extract core names you put in in Zen, you might want to try Split Scenes (Write Files) in the Processing menu. It will give you a ton of files, but if you labeled specific tiles/positions/etc, there should be a checkbox to include that information in the file name.
Ah, I suppose you could do two different cell-based classifiers, and if they work, great! It hasn’t been my experience that those sorts of things are reliable between stains (due to variability in fixation, staining, bleedthrough between stains, etc), so definitely do a lot of double checking.
That said, the two ways to go about it would be to use one classifier for tumor vs stroma. If it is one of the machine learning classifiers, you can just use the runClassifier(“path here”) command to run an initial command, and then possibly use derived classes (read more here) to differentiate between positive and negative for each of the tumor/stroma types.
Another way would be to use a more granular approach (my preference) and after classifying an object, set a new variable. For example, after running the tumor/stroma classifier (which you would just access the same file path in every project), you would use putMeasurement to create a new “Tumor” measurement that would be “1” for tumor or “0” for stroma. Or maybe -1 if you have some criteria for excluding cells. Then run the second classifier. The cell’s “class” would hold the marker classification information, and the Tumor variable would determine whether that cell was considered to be in the tumor.
More on adding measurements here. And maybe specifically this one as an example, where you would check the cell’s class, and then put the new measurement within the loop.
I prefer that type of method, because if you later decide you want to rerun a classifier, you can pick which half of the classification to target independently (though if you redo the tumor/stroma, you would want to create another putMeasurement for the other marker classes).