Configuring MONAILabel and CVAT running in separate docker?

[bilalcodehub]

Hi All,

MONAILabel and CVAT versions: Latest

I want to use MONAILabel for surgical video annotation. I can only install the software in docker. I installed MONAILabel docker and checked it through the radiology app using 3D Slicer, so both are working perfectly.

For surgical videos, I need to install CVAT which I did through docker. Now I have two dockers with one running MONAILabel and another CVAT. How can I configure CVAT & MONAILabel in this setting so that they work with each other for video labeling?

I will greatly appreciate your help on this.

Thanks in advance
Bil

[tangy5]

You can refer to this page: https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/cvat#installation
The "deploy" script will deploy MONAI Label models to use in CVAT.

For a full instruction, step-by-step instation of MONAI Label, CVAT, Nuclio sutff, here is a tutorial: https://github.com/Project-MONAI/tutorials/blob/main/monailabel/monailabel_endoscopy_cvat_tooltracking.ipynb

But I feel you already done the CVAT installation, just need the "deploy" step.

Hope this helps.

[bilalcodehub]

Thanks @tangy5 for the response and for sharing such a detailed tutorial. Much appreciated.

When I run this ./deploy command, I get the error saying no such file or directory. Please check the screenshot below:

Any idea why this might be the issue?

[tangy5]

Hi @bilalcodehub , the file is not a part of CVAT. It's a "plugin" developed by MONAI Label team.
The file is here: https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/cvat/endoscopy

You can read the tutorial or the Github page for more details, such as how to get them.

[bilalcodehub]

Hi @tangy5: I see these files are copied from monailabel plugins folder to the workspace folder created on the local computer with following command:
docker cp $(docker container ls | grep 'nvcr.io/nvidia/clara/monai-toolkit' | awk '{print $1}'):/opt/conda/monailabel/plugins/cvat workspace

In my installation, MONAILabel is running through the docker container, not installed on the local system so can't run the above command as the docker container ls | grep 'nvcr.io/nvidia/clara/monai-toolkit part of the command is returning an error when I run it on the docker with MONAILabel. Do I simply grab plugins from MONAILabel GitHub as the tutorial describes in the next step and deploy them to CVAT?

Apologies for naivety as this is the first time I am using MONAILabel and appreciate any guidance on this.

[tangy5]

Ok, in this case, you can refer to option 2 in the tutorial, in the docker, you can either pull the file or mount the file to the docker.

git clone https://github.com/Project-MONAI/MONAILabel.git
Deploy all endoscopy models
./MONAILabel/plugins/cvat/deploy.sh endoscopy

[bilalcodehub]

I was able to run the option 1 command and copy the files from docker. The docker name is different on my computer so I needed to adjust the command as follows:
docker cp $(docker container ls | grep 'projectmonai/monailabel:latest' | awk '{print $1}'):/opt/conda/monailabel/plugins/cvat workspace
Thanks for the help.