While using CellProfiler (3.1.9) to analyze images with numerous cells, I stumbled on a label issue!
I need to continue the processing in FIJI, and thus I thought I will re-use @NicoKiaru’s code
But the CellProfiler’s output has multiple objects with the same label value (@CellProfilerTeam can something be done about it ?) thus I thought to use the particles analyzer to get different ROIs.
This script does the job, but the way we get rid of the “0” label (with RGB image) is a bit hacky/dummy and I was hoping for your help to come up with something better !
Here is a macro snippet to get a label image from blob
// macro to generate an image with labels run("Blobs (25K)"); setAutoThreshold("Default"); setOption("BlackBackground", true); run("Convert to Mask"); run("Analyze Particles...", " show=[Count Masks] exclude ");
You can download Here is a larger image from CellProfiler corresponding to the preview below.
Thank you in advance for your inputs,