I’ve been spending the last couple of days reading Ilastik’s manual and playing around with it. I’m really impressed and I’m rather optimistic that it can help me, but I’m still not sure if and how it can, so I wondered if you could help me out here
The image I’ve attached is of an intestinal section; red is the nuclei, blue marks the intestinal epithelium, and green marks a subset of the intestinal epithelium. My goal is to quantify the number of cells in green and normalize it to the number of all epithelial (blue cells), or at least to the length/area covered by the epithelial cells, and to do that over a large amount of images.
I have three pressing questions at the moment:
- Is it possible to do that with Ilastik? So far I’ve been able to use the pixel identification and the segmentation applets on a few images to mark the green cells individualy and accurately, as well as to mark the area covered by the blue cells, though, for now, not as individual cells. Do you think it would be possible to use Ilastik to count the number of individual blue cells with a reasonable accuracy?
- Let’s say that I have 20 images and I wish to use 5 of them to train “Ilastik” to identify my cells of interest, and then let the program automatically identify these cell types in the remaining 15 images based on the training I’ve provided in the first 5 images. How do I that, technically?
- How do I get the program to count specifically the green cells which are also blue (i.e. green epithelial cells), but not (or separately from) the green cells which don’t fluoresce in the blue channel (i.e. green cells which are not epithelium)?
Looking forward to hearing from you
562651750824016 - without EGFP.tif (10.7 MB)