Compatibility issues upgrading 2.2.0 project to 3.0


#1

Hello,
I had some issues when importing my CellProfiler 2.2.0 project into CellProfiler 3.0 and need some help figuring them out. I’ve attached my original project, the attempted upgrade, and an image set. Any help would be greatly appreciated.

Here are the issues that I have no idea how to fix (object names are in parenthesis):

IdentifyPrimaryObjects (uDNA): did not flag as anything wrong, but now my objects are way smaller. Could it be the smoothing scale?
IdentifyPrimaryObjects (CenterMembFill): Threshold strategy previously was binary image, no longer an option. Tried changing to Otsu, but now I have no objects. What would give me the same results as binary image?

Here are the issues I think I fixed (let me know if I did something that might be an issue for me later):
IdentifyPrimaryObjects (uMemb): Previously used automatic thresholding, option no longer available. Changed to Global, Otsu, two classes with smoothing, and correction factor of 1. Seems like it worked (have only tried one image), is there anything else that should be changed to be closest to what I had before.
IdentifySecondaryObjects (OuterMemb): Thresholding set to default instead of Otsu. Size of adaptive window used to be calculated based on Image size, no longer an option. Changed the thresholding to Otsu two classes and seemed to work out ok.
IdentifySecondaryObjects (uCellsbyMemb): Wrong image was selected. Thresholding set to default instead of Otsu. Size of adaptive window used to be calculated based on Image size, no longer an option. Set the thresholding back to otsu two classes with no smoothing and selected the correct image. It appears to be working.
OverlayOutlines: All of my objects were deselected, seems to be a difference in how the object names are handled in this version. Selecting the correct object fixed everything.

Google drive link to images (they wouldn’t attach properly):
https://drive.google.com/drive/folders/17zpVt38snqcKtHYWSyzjnVS4RnPHcoGd?usp=sharing


#2

Hi,

I don’t have time at the moment to go through your pipeline line by line (hopefully someone else will), but let me point you at this blog post on changes to make when converting pipelines to 3.0 and this forum thread on replacing binary image thresholding. I think they might help solve your issue!


#3

Thanks so much! Shifting to manual (and switching to not filling holes in the object) with a tiny number fixed the binary theshold issue. The other issue was a difference in the new thresholding and all I had to do was change the threshold correction factor. Everything appears to be working now!


#4

Awesome, glad to hear it!