Having trouble using 3D analysis

cellprofiler

#1

Hi Guys,
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!


#2

Hi,

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.