Anyone know a good pipeline for processing DIC images so that the individual cells can be found using analyze particles? For example, in this image, https://imgur.com/a/FcED5eX, I would like to get each individual cell to be an ROI.
DIC can get a little tricky because of the contrast mechanism. I generally have luck messing around with edge filters in these cases (Process -> find Edges). I’d recommend trying that with some thresholding (ctrl+shift+T) and some of the Binary operations (Process -> binary). Analyze Particles should work from there.
Let me know if you have any luck.
i have actually done that successfully, the only problem is sometimes fails spectacularly and most of the time misses quite a few cells.
My current pipeline is:
- find edges
- convert to binary
- close or dilate to close some of the holes in the binary
- fill holes
- watershed algorithm to split up blobs
- analyze particles
can you post an example result?
also may be worth considering some attempts from people previously. I found this post on the forum that might be helpful:
did you try dilating and closing multiple times before filling holes? That might help a little bit here. Not sure how repeatable that might be.
It doesn’t seem horribly far off. you might be able to get it to work.
I mean it works, its just bad. I would like to improve it somehow
Sorry for the delay, but I had an idea i figured was worth suggesting. Weka segmentation plugin might work well for this. have you given that a shot?