Welcome to SlicerMorph

Our project aims to enhance the open-source 3D Slicer platform with cutting-edge tools to assist biologists, anthropologists, and morphologists in analyzing 3D data from research imaging modalities. Our ultimate goal is to foster a collaborative community within the 3D Slicer ecosystem to facilitate seamless data exchange and promote the advancement of open science.

SlicerMorph streamlines digital morphology research by enabling effortless data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application. Say goodbye to multiple programs, different file formats, and workflows!

Getting started with SlicerMorph

If you are not familiar with the 3D Slicer or looking for a free (and open-source) alternative to commercial 3D visualization programs, you can start by downloading Slicer from http://download.slicer.org. Please use the latest stable version. After installing Slicer, use the extension manager to search for and install SlicerMorph. This is the official method of obtaining SlicerMorph, which will give you the most up-to-date version.
Follow this link for more detailed installation instructions

Documentation and Self Help

Some additional tutorials

SlicerMorph Ecosystem

While started primarily as an extension to import microCT scans and conduct Procrustes analysis, SlicerMorph Project has now many other extensions that facilitate different types of 3D morphology and morphometrics workflow. Checkout:

Also, check out the MorphoCloud On Demand Instances that allow you running SlicerMorph inside a web browser on the cloud using powerful virtual computers. Once the instance is up and running, all the SlicerMorph extensions are preloaded and ready to be used. You can simply drag and drop your datasets from your local computer onto browser window running your MorphoCloud session and they will be ready to be used.

How to Cite SlicerMorph Project

If you used SlicerMorph and its related extensions in your project, please give citation to one or more of the following papers:

Events

Recurring Online SlicerMorph User Group Meeting

Join us via online every 1st Wednesday of the month at 9PST (please join the mailing list for the meeting link)

Upcoming Events

  • January 3rd, 2026 MorphoCloud and MorphoDepot short course at SICB (Portland, OR)
  • January 4-5th, 2026 MorphoCloud and MorphoDepot presentations SICB (Portland, OR)

    • Past Events

    Contact

    Funding acknowledgement

    SlicerMorph was initially supported by an NSF Advances in Biological Informatics grant to Murat Maga (ABI-1759883). SlicerMorph ecosystem and MorphoCloud infrastructure are now supported by funding from National Science Foundation (DBI/2301405), National Institutes of Health (HD104435) and ACCESS Cyberinfrastructure allocation (BIO180006) to Murat Maga.