Create subfolders in the output directory

I have problem using the funtion “Create subfolders in the input folder” in the SaveImages module. I’m using a pipeline to merge two images using GrayToColor module and then save them with the SaveImages module.
I’ve checked the box next to “Create subfolders in the input folder” to have the same subfolders structure as the input folder, but CellProfiler never creates any folders. It just save the first image directly in the ouptut folder and the ask me if I want to overwrite the file for every other images it has to save. I’m not sure if this is a bug or if I must do something special to make it works…
I’m using the beta v. 9978 of Cellprofiler 2



This is indeed a bug, which I have reported. I’ll post back here when it’s completed and released.

A workaround is to do the following:

  • LoadImages with metadata extraction from the path. You can then reference the folders below the input folder as a metdata tag.

  • SaveImages with the output file location set to Default Output Folder sub-folder
    and the subfolder entered using the metdata tag from LoadImages. This will create the subfolders with the same name as those from the input folder.

If you’re unfamiliar with metadata tags, you can look at the Help for LoadImages and SaveImages, or refer to Help > General Help > Using metadata in CellProfiler from the main menu bar.

Our latest release, r10415, fixes this issue.