MorphoDepot logo MorphoDepot
⚠ Work in progress. Lab onboarding and the MorphoDepot organization are still in development and not yet open to the public.

Collaborative 3D anatomical segmentation, built on GitHub

MorphoDepot brings the fork-and-contribute workflow of open-source software to the segmentation of 3D specimen scans — so labs and contributors can build, review, and version anatomical datasets together.

Onboard your lab How it works →
Get started on MorphoCloud → Slicer extension → Tutorial →

What is MorphoDepot?

MorphoDepot is an open platform for the collaborative segmentation of 3D specimen data (CT, microCT, and other volumetric scans). It pairs a 3D Slicer extension with a GitHub organization, so each dataset lives in its own repository: the source volume is stored as a release asset, and every segmentation is a versioned file contributed, reviewed, and released through ordinary GitHub branches and pull requests.

The result is a transparent, attributable, and reproducible record of who segmented what — the same collaboration model that powers open-source software, applied to anatomy.

How it works

The MorphoDepot workflow: a source 3D volume is published to a GitHub repository, contributors fork it and submit segmentations as pull requests, and reviewers merge and release versioned baselines.
The MorphoDepot workflow at a glance.
  1. Install 3D Slicer and add the MorphoDepot extension from the Extensions Manager — or skip setup entirely on MorphoCloud, where it's pre-installed.
  2. Running a lab? Onboard at join.morphodepot.org with your ORCID iD to set up your lab team in the MorphoDepot organization. WIP — not active yet
  3. Contributing segmentations? Browse the public repositories, claim an issue, and submit your work as a pull request directly from the extension — no onboarding needed.

Read the full tutorial Step-by-step, with screenshots.

Who it's for

Labs & PIs

Run segmentation projects

  • Create and own dataset repositories
  • Manage contributors on your lab team
  • Review submissions and release baselines
Onboard at join.morphodepot.org

WIP — not active yet Organization onboarding is in development and not yet open.

Students & contributors

Segment & contribute

  • No organization membership required
  • Work on any public MorphoDepot repository
  • Open an issue, fork, and submit a pull request
Get the Slicer extension

Events

Aug 6–7 2026

Teaching 3D Morphology with SlicerMorph and MorphoCloud

Online workshop · 9 a.m.–1 p.m. Seattle time

A two-day workshop: Day 1 covers MorphoCloud operations and setup customization; Day 2 covers using MorphoDepot to assign and monitor 3D segmentation tasks. Register for either day — Day 1 is a prerequisite for Day 2.

Register

Resources

Citation

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