apologies in advance for the noob question, I am new to the field and a bit overwhelmed by the amount of tools available.
My goal: I would like to manually correct several segmentations made with Stardist (directly in Python for sake of automation). What I have are tiff files where pixels have value 0 if they belong to the background, 1 to n if they belong to cluster/cell/nucleus 1 to n
My problem: all the software I found so far allow to create a segmentation by hand from scratch with more or less practical tools (so far what I like the most is QuPath and its brush) but I got nothing that allows me to open the base image, load the Stardist segmentation on top and work on that, ideally with some sort of brush tool. The closest thing I found so far is the promising Caliban by the Van Valen Lab, but something easier to install and operate would be extremely welcome.
I was thinking of doing this directly in Photoshop, but:
a) I would be happier to find an open source solution/Fiji plugin,
b) with PS I wouldn’t know how to add a color mapping to the segments layer so to have it as the usual happy patchwork of colors rather than a black file with almost black spots as it would be naturally read.
Attached, just to give you a flavor of the order of magnitude of the “errors” I need to correct, a tetraptych consisting of:
- Grayscale nuclei channel used by Stardist,
- same as 1) with its Stardist segmentation superimposed, as a raster layer,
- nuclei and membrane channels
- same as 3) but with segments as seen by Stardist (centroids, boundaries)
Thank you all in advance for the help and the patience. Hopefully I didn’t cause any heart attack by misusing the terminology or so.