MorphoCloud On-Demand Instances: Run 3D Slicer and SlicerMorph inside a web browser.

Powerful virtual machines (compute instances) that provide interactive remote desktop interface with 3D Slicer and SlicerMorph and its related extensions preloaded for 3D digital morphology and morphometrics data processing.

In a nutshell, you:

1. Have a research and/or teaching focus centered on 3D biological structure (e.g., 3D morphometrics, or visualization);
2. Need occasional access to powerful computers with large amounts of RAM and GPU (up to 40GB GPU)
3. You have a github account;
4. You have an ORCID with a public profile.

Also, note that any use case falls under the category of Human Subject Research is not allowed on MorphoCloud.

To get more information about these instances, please review this document.

Available Instance Types

Flavor	RAM	Cores	GPU	Storage
g3.l**	60GB	16	A100 (20GB)	100GB
g3.xl	125GB	32	A100 (40GB)	100GB
m3.x	250GB	64	None	100GB
r3.l	500GB	64	None	100GB
r3.xl	1000GB	128	None	100GB

**g3.l is the default flavor.
Click to see the approximate (delayed 5 minutes) count of available resources on JS2

MorphoCloud Commands

Command	Description	Who can run
/shelve	Shelve (turn off) the instance.	Issue creator, Admin
/unshelve	Unshelve (turn on) the instance.	Issue creator, Admin
/encode_email	Update issue description obfuscating emails.	Issue creator, Admin
/decode_email	Update issue description deobfuscating emails.	Issue creator, Admin
/email	Send email to Issue creator with connection URL (only possible if instance is active)	Issue creator, Admin
/renew	Extend the instance lifespan if additional time is available.	Issue creator, Admin
/create	Approve the request and then e the instance and the volume.	Admin
/delete_instance	Delete the instance.	Admin
/delete_volume	Delete the storage volume.	Admin
/delete_all	Delete the instance and volume.	Admin

Ready to give a try?

Go to https://github.com/MorphoCloud/MorphoCloudInstances/issues/new/choose, click Get Started and fill in the issue template and choose your instance flavor. Your request will be approved within 24h (often faster).

MorphoCloud Desktop Interface

• A: Side toolbar that gets activated by pressing the CTRL (or CMD) + ALT + SHIFT keys. It allows copy/paste into the remote session, browse and download files on the remote drive and adjust screen zoom levels (cut from the screenshot).

• B: Shortcuts to commonly used applications and to MyData storage volume.

• C: Displays list of available applications (searchable)

• D: Right mouse clicking anywhere on desktop brings this menu, including changing screen resolution (Display settings).

• E: Click on this icon anytime to extend your session for additional 4 hours.

MorphoCloud Instances performance and troubleshooting common issues

• While the web browser based connection to MorphoCloud instances is the most convenient way, its performance may vary. Particularly if you are a using high-resolution monitor, application and desktop scaling might be less than ideal. For better performance, we suggest using the dedicated TurboVNC client, which is freely available at https://github.com/TurboVNC/turbovnc/releases. Then, choose the appropriate executable for your operating system. Once the TurboVNC is installed, you can connect to your running instance using the convention: W.X.Y.Z:1, where W.X.Y.Z is the IP address of the instance provided in the email. You will use the same passphrase as the connection password. You can also check the email sent by the MorphoCloudPortal for more instructions on using TurboVNC.

• If the 3D rendering performance appears slow, you need to make sure: (1) 3D Slicer is actually using the GPU, and (2) GPU on the instance is function. For the first issue, make sure you are always launching the Slicer from the shortcut on the desktop. For the latter, open a terminal window and type the command nvidia-smi. This should list the GPU in your system, its driver and CUDA version, along with the applications using it (e.g., if Slicer is running, it should be listed). If there is any error, please copy and paste the full screenshot and notify us. Sometimes rebooting the system from the command line via the command sudo reboot, helps clear the issue.

Funding & Acknowledgement

MorphoCloud services, including MorphoCloud OnDemand Instances, are supported by funding from 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 by 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 cyberinstructure supported by grants from National Science Foundation (MorphoCloud: DBI/2301405; JetStream2: OAC/2005506; Exosphere: TI/2229642) and National Institutes of Health (MorphoCloud: NICHD HD104435).”