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MorphoDepot: Collaborative segmentation projects

Key Investigators

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

Presenter location: In-person

Project Description

We are developing tools for segmentation of biological specimens (e.g. 3D microCT of fish or snakes). The idea is that a Lab Director will define a project, such as what scan to segment, what anatomical structures to segment, the terminologies to use, etc. Students or lab members would be assigned to segment subsets of the data. We want to leverage existing data management tools, such as github for organizing issues and contributions, and jetstream2 for hosting data and computation.

We are interested in facilitating collaborative segmentation, including dividing a whole project into tasks, managing allocation to tasks to segmenters, managing/merging contributions, etc.

If you are interested in similar topics, please join our project!

Objective

1. Networking: we would like to know how this fits with anyone else’s projects and possibly collaborate
2. Exploration: test the use of github for managing segmentations and zarr with s3 back end for large data
3. Refine: based on what we learn, iterate on the concepts and implementation options

Approach and Plan

1. Try zarr on ceph in jetstream2 and zarr in Slicer.
2. Try storing seg.nrrd files in github repos
3. Try skeleton Slicer module

Progress and Next Steps

1. Describe specific steps you have actually done.

Illustrations

No response

Background and References

No response