Path to aligned images in CPA?


Hi again,

I have a pixelshift in my images which I automatically correct using “Align” in my CP pipeline. Later on, I save the aligned images and perform the analysis on them. Now I started to use CPA, but it would open the unaligned images and just one aligned image (grid_cropped_aligned_corrpow2) only. Which - of course - is not very meaningful. I have tried to change the settings in the CPA properties file, but it did not work as the path to the aligned images is not stored in the database (the aligned images are stored in the input folder but they have a different name).
Do you have any suggestions how I could save the path to the aligned images? Or any other workaround? (6.6 KB)
CellProfilerTestMicropattern v9.4 LIP.cpproj (745.2 KB) (1.9 MB)


Hi Beneedict-

I’ve been trying to troubleshoot the same thing. The farthest I got was to add a SaveImages step in my CP pipeline, which then writes the aligned images to my filesystem. I then tried to incorporate those pathnames into my properties file but couldn’t get CPA to load those images. I’m not sure I got that bit right, though.

Confusingly, the ExportToDatabase step in CP has a box where you can select which images to make thumbnails out of…but this either doesn’t work as intended or does something different that what I’m expecting. I have my aligned images selected in this step, but it’s the raw images that get shown in CPA.

If you or someone else gets this working I’d love to hear about.


Thank you bfeng,
I am actually stuck at the very same point in the process! I hope, somebody can tip us off :slight_smile:


In SaveImages for the Aligned images, have you checked the box near the end of the settings that says something like Save Path…? I don’t have CP accessible right now so I’m just guessing, but that setting is where the path gets input into the database and then into your properties file. The thumbnails are only used in PlateViewer I believe, and not for Classifier.


“Record the file and path information to the saved image?” that’s it! Thank you so much, it works great!


I had that box checked but I was still having problems. Beneedict, if you got this working could you attach your properties file and comment where you modified it to use the new paths?

Glad someone got this working!



Hi Brian,
I have labelled the modified properties sections in the uploaded (2.7 KB) in red!
Basically, you have to give the path and the files using the name of the image (the CP internal one, not the full name of the exported image) with Image_PathName_ / Image_FileName_ as prefix e.g. “Image_PathName_cells”.
The other stuff is just the names which CPA is going to display and the colours ist should pre-set the channels to.

Good luck!

P.S.: the updated pipeline: CellProfilerTestMicropattern v9.4 LIP.cpproj (747.7 KB)


Thanks for your pipeline and property file. I was also able to get this working!