I found the example wound healing CP pipeline very helpful in segmenting images from these assays. The pipeline does well in cases where there’s a visible scratch/wound but I find that it needs some tweaking for cases where the wound is nearly filled in the later time points of these assays. Attached is the original image (CPImage.jpg) and the analysis result I get from CP (CPResult.png). The analysis attached was generated using the built-in pipeline except I modified the ‘Typical artifact diameter’ to 10 in the Gaussian filter “Smooth” step.
It looks like the darker regions of the image get segmented as objects. What is the strategy for avoiding this? Is there a pre-processing step I could add that equalizes the contrast/brightness perhaps? Or is it more likely to weak by tweaking the object finding parts of the pipeline? Thanks.