Output structure expected in the Docker file

Hello,

The structure of the output files expected is not really clear: from what I understood, we need to output 3 files per patient: detected-lymphocytes.json, detected-monocytes.json and detected-inflammatory-cells.json. Should these files be stored in the /output folder during the docker execution ? And how should we separate json files from different patients ? (should we create subfolders with the patient id ex: A_P00001 in the /output folder ?).

Thx a lot for your help.

Please have a look at the example inference code on GitHub here to see how to save the files.

Grand Challenge processes each file in parallel, and they are all saved separately per case in a folder with the anonymized ID. So, all you need to do is save the JSON files into the /output folder.