Having trouble using 3D analysis

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!

1 Like

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.

Hello I am having the same issue with this error message, did you ever figure it out? Thanks!

Hi @mquintero,

I have encountered this error earlier but when I changed the shape & size, it worked fine. Also made a changes in other modules like (“Watershed”). Actually it depends on the pipeline that your are trying with.
As mentioned in earlier thread, we could help you better if you could share the sample image & a pipeline in which you face the issue.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

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