How to make a image file from monailabel inference?

Hi I want to make an inference image file from monailabel training model(pathological image using qupath), but it only provides the json format I think.

(When I connect to the monailabel local server, upload the trained model and push the inference, it only output the json although I set up the image flag on the output flag.)

How can I get the image from the monailabel server ?

Hi @seung-hyoung-ko,

Sorry for the late response.

The regions are represented by ASAP - Automated Slide Analysis Platform (https://github.com/computationalpathologygroup/ASAP). That's why you have an XML file for this.

Here you can see the code we use to convert it on the viewer side:

MONAILabel/plugins/qupath/src/main/java/qupath/lib/extension/monailabel/commands/SubmitLabel.java

Line 160 in 5e9732e

    
           private Path getAnnotationsXml(String image, ImageData<BufferedImage> imageData, int[] bbox)

and from the server side: https://github.com/Project-MONAI/MONAILabel/blob/main/monailabel/utils/others/pathology.py#L92

I guess what you mean is converting the polygons into a label mask. Is there a reason to do this?