I’ve created a pipeline for identifying any white colored regions and apply them as masks so as to be able to reduce the area of non-tissue that is being analysed.
I’ve tried using Unmix Colours and had pretty good results, but have since opted for ColorToGray with the subsequent step being ImageMath in order to increase the image contrast, followed by an additional ImageMath to rescale the intensity levels.
I then use IdentifyPrimaryObject in order to locate all white regions, and output this image a mask that is used for downstream analysis. It works very well overall; however, for some reasons it counts some non-white regions as white. I’ve attached an example image where a couple of cells that are strongly non-white, are included in the masked region.
Any thoughts on how to improve the pipeline? I’ve tried using both .jpeg, .tif, but to no avail.
I’ve marked two cells with red squares in the attached image. These are cells that are are incorrectly included in the white region (there may of course be more like this).
WhiteArea.cppipe (9.3 KB)