MONAI Label extension in Qupath (pathology app startup failed)

[CZXHPB]

Dear friends： I want to install MONAI Label extension in the Qupath for efficient annotation, but the extension cannot work well (pathology application startup failed). The picture shows an error message. How can I solve it? I have tried to consult chatGPT, but it still didn’t work out. Thanks!

[tangy5]

Hi @CZXHPB , I didn't see this error before, but see the error logs, it seems some files are missing causing the mailable start server to fail. You could do a clean install with the latest mailable release candidate by:

pip install monailabel==0.7.0rc7

In particular, the "import lib.configs" issue might be from the sample app, make sure the sample app pathology is from the latest.

Let me know if the start server still failing, I can investigate, especially by testing it on Windows machines.

Thanks.

[CZXHPB]

Hi @CZXHPB , I didn't see this error before, but see the error logs, it seems some files are missing causing the mailable start server to fail. You could do a clean install with the latest mailable release candidate by:

pip install monailabel==0.7.0rc7

In particular, the "import lib.configs" issue might be from the sample app, make sure the sample app pathology is from the latest.

Let me know if the start server still failing, I can investigate, especially by testing it on Windows machines.

Thanks.

Dear @tangy5 Thanks for your kind reply. I have updated monailabel to 0.7.0rc7, but the pathology app still failing. I am a beginner of code and python and I have spent three days to solve this issue. To be honest, this issue is driving me crazy. Could you please give me more help? Thanks again!

[tangy5]

From the screenshot, it seems a package called OpenSlide is not properly installed. Can you install it and re-try?

pip install openslide-python

https://openslide.org/docs/windows/

[CZXHPB]

Thanks！@tangy5 I have re-installed and retried many many times, but the error is still the same and the pathology app could not start. It is very strange that the radiology app works well.

[tangy5]

There is nothing with monailabel, it's the 'libopenslide-0.dll' issue on your machine. You could refer to openslide installation Q&As.

Or you can directly use monailabel docker instead of pip .

docker run -it --rm --gpus all --ipc=host --net=host -v ~:/workspace/ projectmonai/monailabel:latest bash

then run monailabel start server command in the Docker bash, but remember you will need the Docker host IP to connect to QuPath.

[zmsunnyday]

Hi, There are some problems with openslide on Windows. You could try to solve this by following this thread https://github.com/Project-MONAI/MONAILabel/issues/683#issuecomment-1348234061

[hubutui]

zmsunnyday has pointed out the solution. Or you could also run monailabel on Linux.