I am trying to find an automated method of automatically cropping the exterior of a well from the ROI (see example image here).
I have tried several iterations within CP to apply a threshold that produces a masked image, but it also tends to remove the cell nuclei signals from the image since they have similar intensity to the exterior of the well. I cannot use a predetermined mask as the well locations are variable, and we lose a signifiant portion of each well if we use a single masking template. Here is the pipeline I have been trying out, based on the results from this thread.
Any help or guidance would be very welcome! Thank you so much in advance!