MorphoCloud provides on-demand cloud instances and reusable GitHub workflows to support computational morphology, 3D morphometrics, and biomedical imaging research.
It allows researchers and educators to launch powerful JetStream2 virtual machines — preloaded with 3D Slicer and SlicerMorph — by simply opening and commenting on GitHub issues.
✨ What You Can Do with MorphoCloud
- Run Slicer in your browser: GPU-enabled remote desktops with up to 40GB GPUs and 1TB RAM.
- Request and manage instances with GitHub Issues: no portals, no manual provisioning.
- Automated lifecycle management: Create, shelve, unshelve, renew, or delete
instances via simple
/commands. - Integrate workflows into your project: Use MorphoCloudWorkflow to vendorize and customize provisioning logic for your community.
- Support research and teaching: Ideal for occasional high-performance computing needs in morphology and imaging.
🖥️ Available Instance Types
| Flavor | RAM | Cores | GPU | Storage | Use Cases |
|---|---|---|---|---|---|
| g3.l* | 60GB | 16 | A100 (20GB) | 100GB | General purpose morphology and morphometrics |
| g3.xl | 125GB | 32 | A100 (40GB) | 100GB | Photogrammetry, NNInteractive, AI applications |
| m3.x | 250GB | 64 | None | 100GB | Computationally intense tasks that don’t require GPU; eg., Image registration with ANTsPy |
| r3.l | 500GB | 64 | None | 100GB | Image registration with larger dataset |
| r3.xl | 1000GB | 128 | None | 100GB | Image registration with larger dataset |
*g3.l is the default instance and is usually more available than other instance flavors.
Check real-time JetStream2 resource availability →
Important Note: Storage refers the persistent storage volume located on /media/volume/MyData. This is where you should keep all your files. The root file system (where your Desktop, Documents, Downloads) folder are located is very small, and if it fills up your instance my function erratically, or not function at all. Make sure you move or create all your files in your /media/volume/MyData storage volume.
🔑 Commands
Once approved, you can control your instance from the issue itself:
| Command | Description |
|---|---|
/create |
Provision a new instance |
/shelve |
Suspend (turn off) instance |
/unshelve |
Resume shelved instance |
/delete_instance |
Delete an instance |
/delete_volume |
Remove associated storage |
/renew |
Extend lifespan of instance by another 60 days (one time only) |
/email |
Resend access email |
See the full command reference.
Installed Software
| Software/Tool | Description |
|---|---|
| 3D Slicer | v5.10 |
| SlicerMorph | ImageStacks, GPA, ALPACA, and other tools |
| DeCA | Morphometrics via dense correspondence analysis |
| Photogrammetry | Generate textured 3D models from photographs |
| MorphoDepot | Collaborative segmentation and data sharing |
| MEMOs | AI based organ segmentation for E15 mouse embryos |
| NNInteractive | AI assisted interactive segmentation |
| PyTorch | GPU accelerated tensor library for AI tools |
| R/Rstudio | Provided by JetStream2 |
| Python3 | Provided by JetStream2 |
🚀 Quick Start
-
For Researchers / Educators: 👉 Request an instance via MorphoCloudInstances issue templates. Approval typically takes <24h.
-
For Project Maintainers / Admins 👉 Integrate workflows from MorphoCloudWorkflow into your GitHub projects. See Requirements and Runner setup.
🖼️ Desktop Environment
- Side toolbar (Ctrl/Cmd + Alt + Shift) for file transfers & clipboard.
- Shortcuts for Slicer, SlicerMorph, and MyData storage.
- Right-click menu to adjust resolution and display settings.
- Extend session with one click (+4 hours).
🙏 Funding & Acknowledgments
MorphoCloud services, including MorphoCloud On-Demand Instances, are supported by funding from the National Science Foundation (DBI/2301405) and National Institutes of Health (NICHD/HD104435). MorphoCloud runs on cyberinfrastructure that is made available by current and previous funding from the National Science Foundation (JetStream2: OAC/2005506, Exosphere: TI/2229642). Initial development of SlicerMorph was previously supported by National Science Foundation (DBI/1759883).
If you use any of the MorphoCloud services for your project, please acknowledge our funders with this statement:
This study relied on cyberinfrastructure supported by grants from the National Science Foundation (MorphoCloud: DBI/2301405; JetStream2: OAC/2005506; Exosphere: TI/2229642) and the National Institutes of Health (MorphoCloud: NICHD HD104435).