Save images to different folders depending on class label?


Is there a way to classify an image and save the images to different folders depending on the class label? I know that it is possible to use FlagImage to skip the image set if flagged, and I could of course use one pipeline per class and only save if not flagged, but it would be nice to be able to do this within the same pipeline.


I’m not aware of a way to save classified images into sub-folders with sub-folder names being generated on-the-go.
But what you can do is to use several SaveImages for each class, and in each module add a suffix accordingly.
For e.g. “__class1” , “__class2” suffixes
So in the end, although all images are saved in the same folder, they can be easily distinguished and moved around by command lines.

Probably there is a better way though.


Hi Minh,
Thanks for the reply. Maybe I was a bit unclear. I want to classify the entire image into a specific class and save the image into a folder depending on the class label. Saving all images to the same folder with different suffixes might be an option, but I don’t think using several SaveImages is the way to save the image only once with the right suffix.


Hi Petter,

Yup, but it’s a little wonky and will require you renaming your folders later- you can use the “Default Output Folder sub-folder” option to save by a FlagImage class as a piece of Metadata- so if you had 3 classes you could set the option like this, and (assuming your images perfectly classify into their bins) you’ll end up with 3 subfolders- 100,010, and 001, which will correspond to your Class1, Class2, Class3.


Thanks Beth, that’s a clever trick! I will give it a try. Hopefully, the collaborators will be satisfied with that.


Beth, How do I get CellProfiler to interpret the flag names as Metadata?


Metadata is the default, but it’s based on the flag’s category


The problem was that I tried to write the class labels instead of right-clicking and selecting. Now I have got it working. Thanks!