"Error while preparing for run: Failed to get image sets"

I get the following error:

when trying to load images from a data set even when I move the images from a shared folder onto my desktop. I am comparing a green and blue image channel and when I view the error details, it tells me that the green channel of the bottom 4 images is missing. If I load a different folder of images named very similarly with the same pipeline, then it works fine. However, when I load from this one specific set of images, I get the error.

If I try to remove the offending images from the dataset and analyze, it simply tells me another four images are missing.
The file that it stalls on opens fine in ImageJ.

Am I missing something?


First, what version of CP are you running? 11710 or a newer Trunk Build?

This is likely due to metadata handling. Are you extracting metadata? If you post your pipeline here, that would help us debug.

Also, if you are missing files in either of your channels, so that they don’t have a corresponding image in the other channel, then CellProfiler will complain. We try and locate the “missing” images, however this is not an easy matching task and it may report the incorrect imaging sites at the bottom of your list. You are best to copy a few sites’ worth of images in which you know there are no missing files into a new directory and try running that, or inspect your images very carefully to see if there are any aberrations.

Let us know,

Sorry for being a terrible person and not replying to this sooner! :blush:

This was exactly the problem (2nd paragraph). Thank you for your help!

There was something wrong with one of the channels so it ended up with some corrupted files.

No problem - thanks for your response!