I downloaded the latest release (r11353) which should have fixed an error while using the ‘fill small holes’ operation. This operation doesn’t lead to an error anymore but doesn’t seem to work or it’s possible that I use it incorrectly.
I tried several ways to avoid this step, but from the set of images I have I can’t use the ‘Fill holes in identified objects?’ option in IdentifyPrimaryObjects as in some cases it fills the wound, which is what I’m interested in. The purpose of this assay is indeed to look at the healing of the wound by measuring the cell monolayer area at different times. For this images set, we are using DAPI labelling as marker of the monolayer, and basically dilate it . If I do a lot of dilation / erosion / close steps I end up with too closed wound or remaining holes into the monolayer. I was thinking of inverting the binary image, sieve small areas and inverting again, but haven’t found a sieving operation.
I attached the pipeline and a few images. Thank you for helping me deal with this question…
woundhealing_110719.cp (9.47 KB)