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MorphoDepot discussion and optimization

Key Investigators

• Steve Pieper (Isomics, USA)
• Murat Maga (Seattle Children's, USA)

Project Description

As part of the MorphoCloud project, we have developed a MorphoDepot, as 3D Slicer extension that is already available and in use.

The goals are to help organize work related to 3D imaging, primarily for biological morphology applications. Initial target is segmentation of microCT scans of animals. In the future it could expand to applications like landmarking and other annotation / analysis tasks.

The extension relies heavily on GitHub as the back-end, with each scan being associated with a repository, and segmentation tasks being managed by issues and pull requests. The system is working and is in the early stages of real-world usage and we are collecting feedback about usability.

The system uses the Github CLI, gh, to interact with Github but has some performance issues and sometimes the API is throttled due to quota restrictions.

Objective

1. Make the Project Week community aware of this extension
2. Gather feedback about possible other use cases for similar technology and explore possible collaborations
3. Get ideas about how to improve performance to scale up to more users and repositories.

Approach and Plan

• Give demos to any interested parties
• Discuss github actions and other ways to optimize the gh data process

Progress and Next Steps

• I had a productive discussion with Deepa about how the github repo approach might apply to the multisite ultrasound analysis use case
• I researched the github app approach to centralizing a database cache of repository status, and this seems feasible if still a bit clunky
• More research and refinement is needed to put an actual system in place, but the contraints space is getting clearer (what things can be done with the gh cli vs which things require manual interaction with the github web site)

Illustrations

No response

Background and References

Preprint describing the project: https://arxiv.org/abs/2601.00030