I am attempting to create a masked image that looks something like this (see uploaded image below) where one color designates positive staining (such as staining selected by a threshold) and the other color is just empty or ignored.
I am curious if I can export just the threshold overlay on my image to a program like imageJ where i can then save the image and it will exist in the simple form as seen above?
I know that i could create a mask/binary image that represents positive thresholding in ImageJ quite easily, but I would like to keep the thresholding/annotation part in Qupath if possible as i like the annotation ability to ignore the thresholder’s false positive on staining artifacts. In the image below i have a large outer region and then i annotated smaller areas that i want my thresholder to ignore.
So far I have been able to make an annotation around my tissue of interest, then use my created thresholder to “create objects” and then export that annotation with those objects into imageJ. I am now stuck at this point because the objects that i create are hollow and i’m not sure how i would select just the objects to create a black and white image.
Any suggestions would be awesome, thanks so much!