Run for project, create preset? / preselection

Dear all,

I am using QuPath in a project with 212 images.
Say that some of these images (~20) will be used for some additional analysis, then I can use Run > Run for project and select these images manually.

However, it might be a useful addition if you can make preselections, so that you can add a label or something to these 20 images (for instance ‘sub-study’) and that you can select/add all images with this label at once?
(I know that the selection is maintained if you ‘run for project’ several times, but if you exit and reopen QuPath this selection is not maintained.)

Or is there a workaround for this already available?


There is a search area in the run for project to search for substrings.

If you want to go through the effort, you can rework your scripts to work in terms of projects using Run, rather than for single images using Run for Project, though that can get somewhat involved. Once you get to that point, you could modify the scripts to work on various subsets within the project.

Alternatively, you can use the script you currently have, but include an IF statement at the beginning. “IF” the filename includes “someString”, run this code. You could also use that sort of logic to create one big script that does different things based on the image name.

You could also select groups of files in the Project tab and add Metadata to them (context menu), and use similar logic for the metadata. Rather than checking the file name, check whether the metadata includes a certain value.

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Hi RA, thanks for your reply!
I didn’t know about the Metadata function. That might be closest to adding a label.
Adding an IF statement to either run the script or terminate based on metadata might be the best way to go for me, I’ll try it out!

Best, Justin

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