How to importing bounding boxes for multiple slides?

[Henrik Marklund]

Hi!

I have a csv with bounding boxes that I want to import in to QuPath for multiple slides.

I know how to do this for one slide at the time:

imageData.getHierarchy().addPathObject(annotation, false)

imageData = getCurrentImageData()ode here...

However, when I try and loop over slides this does not work for me:

for (entry in project.getImageList()) {

    def fileData = QuPathGUI.getImageDataFile(project, entry)//

    def hierarchy = PathIO.readHierarchy(fileData)

    // Can use this also: imageData = QPEx.loadImageData(fileData.getAbsolutePath(), true)

   //// code to get annotation ////

    hierarchy.addPathObject(annotation, false)

The code runs and console message is: "Adding XXX to hierarchy". However, when I using the GUI switch to these slides, the annotations are not there.

Any idea of what is going on?

Thanks a lot for your help,

Henrik

[Pete]

Hi Henrik,

It looks like the data files aren't being saved after you add the annotations.

The easiest way to take care of this is to use your original script with Run -> Run for Project and let QuPath take care of reading/saving the data files.

Note that the forum has moved to https://forum.image.sc/tags/qupath - this one is just around for posterity. Better for any further discussion to be at image.sc