Collaborative 3D anatomical segmentation, built on GitHub

MorphoDepot is an open platform for the collaborative segmentation of 3D specimen scans (CT, microCT, and other volumetric data). It pairs a 3D Slicer extension with this GitHub organization: each dataset lives in its own repository, the source volume is stored as a release asset or in cloud storage, and every segmentation is contributed, reviewed, and released through ordinary GitHub branches and pull requests — a transparent, attributable, and reproducible record of who segmented what. A SlicerMorph project.

Head to morphodepot.org to see how it works, browse datasets, and pick your path:

• Lab / PI — join the organization with your ORCID iD to create archival, citable datasets and manage your lab team. (Onboarding is in development — not yet open.)
• Student / contributor — no membership needed. Browse public repositories, claim an issue, and submit segmentations as a pull request straight from the Slicer extension.
• Educator — spin up short-term datasets for classes and workshops.

• Dataset dashboard — live catalog & activity across the public MorphoDepot datasets
• MorphoDepot extension — the 3D Slicer module
• Tutorial — step-by-step walkthrough of the workflow
• Guidelines, terms & governance — how the organization works

If you use MorphoDepot in your research, please cite:

Maga, A. M., Pieper, S., Donatelli, C., Gignac, P. M., Kolmann, M., Noto, C., Summers, A., & Taft, N. (2026). Forking anatomy: How MorphoDepot applies the open-source development model to 3D digital morphology. Methods in Ecology and Evolution. doi.org/10.1111/2041-210x.70342

A SlicerMorph project · Questions? portal@morphocloud.org