Add SlicerCADS extension

[murong-xu]

New extension

Tier 1

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• Extension has a reasonable name (not too general, not too narrow, suggests what the extension is for). The extension name should not start with Slicer (unless it explicitly provides a bridge between Slicer and a tool or library), because it would make it more difficult to find extensions if the name of many started with the same word.
• Repository name is Slicer+ExtensionName (except if the repository that hosts the extension can be also used without Slicer)
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• Extension description summarizes in 1-2 sentences what the extension is usable (should be understandable for non-experts)
• Any known related patents must be mentioned in the extension description.
• LICENSE.txt is present in the repository root and the name of the license is mentioned in extension homepage. We suggest you use a permissive license that includes patent and contribution clauses. This will help protect developers and ensure the code remains freely available. MIT (https://choosealicense.com/licenses/mit/) or Apache (https://choosealicense.com/licenses/apache-2.0/) license is recommended. Read here to learn more about licenses. If source code license is more restrictive for users than MIT, BSD, Apache, or 3D Slicer license then describe the reason for the license choice and include the name of the used license in the extension description.
• Extension URL and revision (scmurl, scmrevision) is correct, consider using a branch name (main, release, ...) instead of a specific git hash to avoid re-submitting pull request whenever the extension is updated
• Extension icon URL is correct (do not use the icon's webpage but the raw data download URL that you get from the download button - it should look something like this: https://raw.githubusercontent.com/user/repo/main/SomeIcon.png)
• Screenshot URLs (screenshoturls) are correct, contains at least one
• Content of submitted json file is consistent with the top-level CMakeLists.txt file in the repository (dependencies, etc. are the same)
• Homepage URL points to valid webpage containing the following:
  • Extension name
  • Short description: 1-2 sentences, which summarizes what the extension is usable for
  • At least one nice, informative image, that illustrates what the extension can do. It may be a screenshot.
  • Description of contained modules: at one sentence for each module
  • Publication: link to publication and/or to PubMed reference (if available)
• Hide unused github features (such as Wiki, Projects, and Discussions, Releases, Packages) in the repository to reduce noise/irrelevant information:
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• The extension is safe:
  • Does not include or download binaries from unreliable sources
  • Does not send any information anywhere without user consent (explicit opt-in is required)

Tier 3

Community-supported extensions.

• Documentation, tutorial, and test data are provided for most modules. A tutorial provides step-by-step description of at least the most typical use case, include a few screenshots. Any sample data sets that is used in tutorials must be registered with the Sample Data module to provide easy access to the user.
• Follows programming and user interface conventions of 3D Slicer (e.g., GUI and logic are separated, usage of popups is minimized, no unnecessary custom GUI styling, etc.)
• The extension can be successfully built and packaged on all supported platforms (Windows, macOS, Linux)
• Maintainers respond to issues and pull request submitted to the extension's repository.
• Maintainers respond to questions directly addressed to him/her via @mention on the Slicer Forum.
• Permissive license is used for the main functions of the extension (recommended Apache or MIT). The extension can provide additional functionality in optional components that are distributed with non-permissive license, but the user has to explicitly approve those before using them (e.g., a pop-up can be displayed that explains the licensing terms and the user has to acknowledge them to proceed).
• All requirements of tiers < 3.

Comments

• The extension has been tested with the Slicer preview release 5.9.0 on Linux.
• When used for the first time (or after a new update), the model weights and codebase will be downloaded automatically from a GitHub repository.
• The code is released under the Apache 2.0 license, and the model weights are under CC BY 4.0.
• Grateful thanks to the developers of the TotalSegmentator extension, the community working on SNOMED-CT, and to those who shared helpful input during NAMIC project weeks 41 and 42.

[pieper]

After I tested on 5.8.1 I saw the readme says this extension was tested with 5.9 from Sept 5, so it makes sense that this PR is for main. We don't have a PyTorch extension currently for the preview so I can test again when that's fixed.

I did notice however that the install process is very long, even when you have a very fast connection. Probably some better progress reporting feedback would be nice.

Also, the install instructions are inside a scroll area that I couldn't fully read by default and it seems the widget is disabled so it's not possible to scroll.

Another thing that I'd suggest is changing the extension name to something like CADSBodySegmentation or similar so that it's easier for people to discover.

I look forward to trying this out!

[lassoan]

I took these notes before @pieper posted his comments, so there may be overlap.

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Thanks for your contribution, the extension looks great!

It could make your extension more discoverable and memorable if had a more descriptive name. For example:

• CADSBodyCTSegmentation
• CADS_CTSegmentation
• CADS_SegmentationBodyCT
• CADS_Segmentation
• CADSSegmentation
• CADSWholeBodyCTSeg

Once a good name is found then we can finalize the repository name, project name in the CMakeLists.txt file, and the .json file name submitted here.

To make the extension simpler and make maintenance and user support easier, I would recommend to use the NNUnet Slicer extension to install nnunet.