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.

Join MorphoDepot How it works →

Get started on MorphoCloud → Browse datasets → 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.

Install 3D Slicer and add the MorphoDepot extension from the Extensions Manager — or skip setup entirely on MorphoCloud, where it's pre-installed.
Running a lab? Join MorphoDepot with your ORCID iD to set up your lab team in the organization.
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.

Two repository types

You choose a dataset's type when you create it, and the choice is permanent.

	Short-term	Archival
Who can create	anyone	organization members only
Where it lives	your personal GitHub account	the MorphoDepot organization
Storage for the scan	GitHub attachment, up to 2 GB	Jetstream2 cloud storage, 10 GB by default
Citable (DOI)	no	yes
Governance	yours alone, delete anytime	community-governed
Best for	teaching, drafts, experiments	lasting, citable datasets

Read the archival guidelines

Who it's for

Labs & PIs

Build anatomical atlases

Create archival dataset repositories in the organization
Grow collaborative, versioned segmentations of your specimens
Review submissions and release citable, DOI-minted baselines

Join MorphoDepot

Enrollment is open — sign in with your ORCID iD to set up your lab team.

Educators & courses

Teach with segmentation

Spin up short-term datasets for classes and workshops
No lasting commitment — keep, hand off, or delete anytime
Students segment and submit straight from 3D Slicer

See the tutorial

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.

Resources

MorphoCloud Fastest way to start — 3D Slicer & the full MorphoDepot toolchain pre-installed
MorphoDepot extension The 3D Slicer module & documentation
Tutorial Step-by-step walkthrough of the workflow
Join MorphoDepot join.morphodepot.org — lab onboarding with your ORCID iD
RepoClerk dashboard Live catalog & activity across the public MorphoDepot datasets
MorphoDepot organization Dataset repositories on GitHub
Archival guidelines How archival datasets work & what membership means
Terms of usage Licensing & acceptable-use terms
Governance Draft How the MorphoDepot community is run
SlicerMorph The project behind MorphoDepot

Funding & Acknowledgement

MorphoDepot is supported by funding from the National Science Foundation (DBI/2301405). It runs on cyberinfrastructure that is made available by current and previous funding from the National Science Foundation (JetStream2: OAC/2005506), which provides the storage backend for archival datasets. Initial development of SlicerMorph was previously supported by the National Science Foundation (DBI/1759883).

If you use MorphoDepot in your research, please cite our paper:

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

Please also acknowledge our funders with this statement:

This study relied on cyberinfrastructure supported by grants from the National Science Foundation (DBI/2301405; JetStream2: OAC/2005506).