Hi, I’ve been trying to load .cif files in cellprofiler.
Originally I couldn’t get the program to recognise the .cif file but I used the solution here Analyzing ImageStream cytometry data with CellProfiler
Now I can load, and even apply processing to the .cif file, however, it seems to treat the .cif file as just a single image (the first cell image on the first channel). I can’t find any way of processing or seeing the other cell/channel images.
I was wondering if there is an example pipeline which uses .cif files as input?
The pipeline provided here https://cellprofiler.org/imagingflowcytometry/ uses the old version of cellprofiler and requires pre-stitching of images with python (which I currently can’t get to work). It would be great if I could just load .cif files directly into cellprofiler.
Thanks for your help!