Contribution to the SlicerMONAIAuto3DSeg extension

rfenioux
Wed, 06 Mar 2024 12:25:47 +0000
Development

There has been an internal effort at Kitware Europe to simplify the use of segmentation models available as MONAI bundles from 3D Slicer.

The goal of this post is to gather some feedback about the best way to share this work.

For this purpose, we are working on a module that allows users to load and run segmentation models from a bundle available locally, or download one from the MONAI model zoo. Our intention is to make this work available to the community, and we initially planned to create a new 3D Slicer extension for this.

However, we realized that our work present an overlap with what offers the SlicerMONAIAuto3DSeg extension (@lassoan), which is why are now pondering whether contributing our work to this project would make more sense. A new extension might be redundant, as both projects aim to provide an easy way to run inference for Monai segmentation models from within 3D Slicer.

Here are some of the features that we could bring, that are not available in SlicerMONAIAuto3DSeg as far as we are aware:

support models distributed as Monai bundles (instead of Auto3DSeg)

load local bundles from disk

retrieve bundles from the Monai Model Zoo

Note that, like SlicerMONAIAuto3DSeg, there are limitations to our work due to the assumptions we need to make about the model (MONAI bundle being very permissive and general, to allow for many different architectures, input/outputs, etc.).

We would love to hear your thoughts about this.

6 posts - 4 participants