Passing annotations to an analysis pipeline


I would like to pass annotations made on an image to an analysis pipeline, however, when I make some annotations in the interface and go to the nuclei classification demo, which ask for an annotations file, I can not select the annotations I have just made on the image. Is there a way to do so?

Thanks in advance!

There isn’t currently a way to do that directly. We’ve had another request to do this, but we haven’t gotten around to coding it.

There is a work-around that doesn’t involve adding code: you can save one or all annotations to a file and then pass that file (either by uploading it back to Girder or specifying it from a path that can be read by the job).

Ideally, we’d add an “annotation” type to the slicer_cli_web module to allow you to select an annotation and pass it through. As a first step to this, we would want a bit of code for that would run in girder_worker that would fetch the annotation from girder (via girder_client). The UI would then be able to pass an annotation ID to that code.

  • David