Develop bundles for the first release [6/1]

[Nic-Ma]

According to the discussion of our internal meeting, would be nice to develop several bundles for the first release [6/1]:

• Spleen segmentation with UNet - @Nic-Ma
• DeepEdit of MONAI label - @diazandr3s
• Swin UNETR segmentation pipeline - @ahatamiz
• DiNTS AutoML pipeline - @dongyang0122
• Detection pipeline - @Can-Zhao
• Pathology tumor detection - @drbeh
• Brats segmentation with SegResNet - @yiheng-wang-nv
• Example to show bundle + NVFlare - @yiheng-wang-nv @YuanTingHsieh
• Example to show bundle + auto-deploy - @ericspod

[yiheng-wang-nv]

Updates:

Nic and I prepared the proposal of how to contribute a bundle (https://github.com/Project-MONAI/MONAI/wiki/Proposal-of-MONAI-Model-Zoo-Contribution-Pipeline).

I will create the bundle of Brats segmentation with SegResNet, and test the whole process soon.

[wyli]

(about the deployment of bundles #4237)

[ericspod]

@aylward Model Zoo discussion is here with list of bundles to prepare and zoo proposal.

[diazandr3s]

Bundle for DeepEdit is here: Project-MONAI/tutorials#694

Waiting for the Model Zoo repo to create the PR :)

[yiheng-wang-nv]

Thanks @diazandr3s for the quick updates. Will let you know after the repo is open asap

[Nic-Ma]

Hi @ericspod ,

Could you please help share some updates and next steps for the auto-deploy part?

Thanks in advance.

[ericspod]

I'm still working on finalising the operator for the App SDK, current work is here. It's using notebooks that create basic MedNIST and Speen segmentation bundles that we can also include in the zoo later.

[ericspod]

@MMelQin is currently spearheading the effort here.

[Nic-Ma]

Hi @ericspod ,

Is there a PR or something there? I want to get the overall understanding first.

Thanks.

[ericspod]

There will be a PR shortly. The key class is here which implements an inference operator initialized with information from the bundle.

[ericspod]

Bundle for the MedNIST GAN example is up: Project-MONAI/model-zoo#31

[ericspod]

Bundle for 2D cardiac segmentation network: Project-MONAI/model-zoo#32

[MMelQin]

I'll be pushing the changes that integrated Eric contribution today to the branch and create a PR with an example supporting the Spleen bundle from Model Zoo.

[ericspod]

@MMelQin has put together this notebook demonstrating the use of MONAI Deploy with bundles through its bundle operator. This uses existing bundles so should tick the box for the item on deploy.

[Nic-Ma]

Glad to know that, cool!
Thanks for the sharing.

[bhashemian]

Pathology tumor detection bundle is merged.

[vikashg]

@Nic-Ma We have decided to build and share a Breast Density Classifier from Mayo Clinic. I am working on it,

[Nic-Ma]

Cool! Glad to see your contribution!

Thanks.