CPA Image Gallery only shows Coloured Squares


I have a problem that is similar to what was described in another post, but I can’t get it resolved.
CellProfiler ran the analysis and stored the results in our MySQL db, but when I then open the Image Gallery in CPA v 2.2.1 using the properties file, it only shows coloured squares instead of thumbnail images or outlines. When I double-click on a square the full version of the correct image IS displayed fine.
How can I get the Image Gallery to display thumbnails for me?

Many thanks in advance.
Kind regards,

attachment: (173.4 KB)
(contains screenshots of the image gallery and terminal output as well as the .cpproj and .properties files used in CP and CPA)


Can you please try:

  • In “ExportToDatabase” : at the “Database type”, instead of choosing “MySQL” , use “SQLite”
  • At the “Select images for which you want to save thumbnails”, instead of choosing “CellOutlines”, try one of the original image, e.g. “illumER” or “illumHoechst”

Let us see if the issue persists. Then we’ll get back to your preferred thumbnail image later.

I have a suspicion that it may be due to the fact that you’ve got 6 channels listed overall but only one set of thumbnails saved; if you try just deleting
image_thumbnail_cols = Image_Thumbnail_CellOutlines
entirely from the properties file (make a copy of the properties file before you try it), does that fix the issue? Alternately, try saving all of the images as thumbnails and see if that helps.

@bcimini: No, unfortunately that does not fix the behaviour, I tried that already.
And I can not store more thumbnails in the db, because then I run into this error again.
I am currently profiling a few images to test @Minh 's proposal.

@Minh: I have applied the changes you propose (SQLite DB and IllumHoechst as thumbnail) and processed a few images with CP and now the thumbnails are correctly displayed in the Image Gallery of CPA (see (52.9 KB)).
I do not quite understand why this now works…
Should I make the same change for the SQL DB pipeline?

Many thanks for your help.
Kind regards,

Glad to hear it works.

My current guess is that when you load the original images (in your very first module “LoadImages”), the image paths are well kept in the final SQL table, and can be correctly loaded.
If during your pipeline, you generate new images (here are those “CellOutlines”), although you saved it in “SaveImage” module, but the path and location where it is saved wasn’t written (or somehow wrongly written) in the SQL table.

If you’re keen on testing this idea, we can do this experiment:

  • Run your pipeline first time, and save some “CellOutlines.png”
  • Run your pipeline second time, now at the first module “LoadImages”, load the newly saved “CellOutlines.png” as images, name them something like “NewlySavedOutlines”.
  • In the “ExportDatabase” of the second run, select the thumbnail with "NewlySavedOutlines"
    Let’s see if it can display.

I’ll think of a more elegant solution… But let’s see if that’s really the case.