Pathology apps cannot read .ndpi file even if I've adjusted MONAILabel/sample-apps/pathology/main.py

[ShangWeiKuo]

I've added .ndpi on the line 190 ( settings.MONAI_LABEL_DATASTORE_FILE_EXT = [".ndpi", ".svs", ".png", ".npy", "*.tif", ".xml"] ) in the MONAILabel/sample-apps/pathology/main.py.

However. When I start MONAI Label Server to launch pathology app, the ndpi files have still not been read by the app as the picture below.

How should I do to adjust the pathology app to make it read .ndpi files ?

[diazandr3s]

Hi @ShangWeiKuo,

This is a good question. Thanks for opening this issue. Actually, you have to add the extension here: https://github.com/Project-MONAI/MONAILabel/blob/1d034726c655102cf612053842b1c45727966612/monailabel/config.py#L71-L80

The change you've made is for when you run the MONAI Label server as a main Python script and without starting the server: https://github.com/Project-MONAI/MONAILabel/blob/main/sample-apps/pathology/main.py#L179-L190

Hope this helps,

[tangy5]

You will also need to check whether the pathology dataloader, whether the backends can actually support ndpi file format. I remember that the OpenSlide backends can open ndpi, but others may not. You could double check the dataloader.