NVIDIA Clara AI-Assisted Annotation Extension

[lassoan (Andras Lasso)]

Just in case somebody comes across this topic now: NVidia Clara AIAA extension is now available in extension manager.

AI-assisted segmentation extension

We are excited to announce that Nvidia AI-assisted segmentation extension is ready to use in latest Slicer Preview Release (rev28686 or later). The extension has been developed by Nvidia, with contributions from Slicer core developers. While there have been other AI-assisted segmentation modules in Slicer (such as DeepInfer, TOMAAT, SlicerCIP), this newest addition uses Nvidia Clara, a toolkit with significant industrial support and sufficient openness for researchers. Few-minute overview video…

[Bruno_Aragao]

Hello,

Does anyone knows why this message appears ? Is there any server configuration to be made?

Thanks

[lassoan (Andras Lasso)]

Sorry, it seems that the latest updates to the extension broke the network communication. It should be fixed by tomorrow but until then you can use this release: https://download.slicer.org/?date=2020-02-20

[pieper (Steve Pieper (Isomics, Inc.))]

Has anyone tried using DeepGrow? @lassoan I recall we talked that it was 2D only, but their documentation implies it’s 3D (@erikziegler pointed this out).

https://docs.nvidia.com/clara/tlt-mi/clara-train-sdk-v3.0/aiaa/key_features.html#deepgrow

[lassoan (Andras Lasso)]

Yes, at the time it was released it was 2D, maybe it is 3D now. However, it does not use any underlying organ model, so it seems to be just another variant of Grow from seeds/Watershed/etc.

Nevertheless, it would be still interesting to try. That would require setting up the latest version of the AIAA server. @pieper if you have time to set it up then I can give you access to the server.

[nanderson (Natalie)]

Hi There I am also getting the error.
“Failed to fetch models from remote server. Make sure server address is correct and <server_uri>/v1/models is accessible in browser”
Using a Windows machine and the url field is blank as advised.
Just downloaded the extension yesterday. How can I resolve?
Thanks a lot

[lassoan (Andras Lasso)]

The server is up and running and works well from Slicer, from a Windows machine (I’ve just tried it now). If you are behind a company or hospital firewall that prevents web requests to go through then you may need to specify the web access proxy as described here.

[nanderson (Natalie)]

Are there any models for segmenting the Bronchi from the lungs?
Thanks a lot

[lassoan (Andras Lasso)]

I’ve updated the demo Slicer AI server to use latest NVidia Clara 3.0 version and uploaded the latest models (NVidia provides over 20 image segmentation models as technology demonstration - you can see the list here: https://ngc.nvidia.com/catalog/collections/nvidia:claratrainframework). You may find the fully automatic lung segmentation model useful.

In addition to this, you may find models at other places that can be loaded into the AIAA server directly, or brought into AIAA compatible format (see instructions for bringing your own model).

[bsmarine (Brett)]

Hi Andras,

Do you know if there are any open-source COVID lung lesion models currently available in Clara, or elsewhere? And are you still providing a server to host models for the general public via AIAA Slicer plug-in?

Hope you are well.

-Brett

[lassoan (Andras Lasso)]

Yes, we still provide the server. We are in the process of switching to Clara 3.0, which has a few COVID related models, for example a fully automatic lung segmentation model. See complete list by clicking on “Download COVID-19 models” button on this page.

[bsmarine (Brett)]

This is great, thank you!

[strakpe]

Hello Andras,

I have just started to explore the possibilities of Clara and its extension to 3DSlicer. I am quite impressed with the concept and how it works together. My main focus of interest is liver segmentation. There are two liver segmentation models provided by Nvidia and also a general 2D Deepgrow method. Unfortunately, I could not find any annotation model for liver which would make the liver segmentation much faster compared to 2D Deepgrow. I saw the annotation models in some older Clara videos by Nvidia but actual NGC catalog does not offer them anymore. Is there any place where I could download them? Or maybe, do you have any recommendations how to create them from the existing segmentation models?

Thank you,

Petr

[lassoan (Andras Lasso)]

@strakpe

r segmentation models provided by Nvidia and also a general 2D Deepgrow method. Unfortunately, I could not find any annotation model for liver which would make the liver segmentation much faster compared to 2D Deepgrow. I saw the annotation models in some older Clara videos by Nvidia but actual NGC catalog

NVidia developed these models as technology demos, but has no intention of maintaining them. Instead, they provide funding to the monai community to create and maintain models that can be used in Clara. I would recommend to check out monai, see what models they have, and maybe ask on their discussion forum about what they recommend for liver segmentation.

[namnh (Nam Nguyễn Hoài)]

Is Nvidia clara aaa support anymore

[lassoan (Andras Lasso)]

We don’t provide a publicly usable NVIDIA-AIAA server anymore. You can set up and use your own server (or can run on any Linux computer that supports docker and has an NVIDIA GPU with at least about 8GB GPU RAM).

However, since its developers do not support NVIDIA-AIAA anymore, I would recommend to use MONAILabel instead.