So I am trying to run some 3D analysis and I am having a hard time 1.Importing the data correctly and 2. Figuring out if I really need to split the channels-my concern with splitting the channels is that then how can I “count” them later. My original file format is in a .zvi but I converted that to a .tif in FIJI. I have followed the instructions on github (https://github.com/CellProfiler/tutorials/tree/master/3d_monolayer) but I run into trouble when I get to Erosion “footprint array has incorrect shape”. If anyone has any suggestions to these questions I would really appreciate it, I honestly feel like I am not even asking the right question so if you need any clarification please let me know. Thanks!
Can you post (or link to Dropbox, GDrive, etc) the pipeline and images that are creating the error? It’s hard to troubleshoot without those.