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