Welcome to SlicerMorph Project

The goal of this NSF funded project is to extend the functionality of the 3D-Slicer Biomedical visualization suite with tools that will help biologists working with 3D specimen data. The toolkit will enable biologists to retrieve, visualize, measure and annotate high-resolution specimen data both from volumetric scans (CTs and MRs) as well as from 3D surface scanners effectively within 3D-Slicer. We expect the first version to be incorporated into Slicer as an extension in Summer 2019.

Updates, announcements, news, etc.

Applications for the 2019 Summer Workshop is now open (deadline May 1st).

Public repository is now online.

Youtube channel for video tutorials

Sign up for low-volume project announcements listserv

March 2019: An online demo of SlicerMorph on March 6th, 2019 @10-12p (PST)
January 2019: SlicerMorph is attending the 30th NA-MIC Project week. See the projects we are involved:

  • Prototype of SlicerMorph.
  • MorphoSource and obtaining 3D specimen data through 3D-Slicer.
  • 3D-Slicer Markup infrastructure redesign.
  • Where to begin?

    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 it from https://download.slicer.org. 3D-Slicer website provides a plethora of documentation. For use cases that involve high-resolution, non-clinical datasets, you can look at these following tutorials. More will be added along the way.

    1. A detailed example of showcasing existing functionality in 3D-Slicer.
    2. Obtaining 3D image stacks from MorphoSource and processing them in 3D-Slicer.
    3. How to exchange complex projects with colleagues.
    4. How to import Scanco microCT datasets into 3D-Slicer.
    5. Using landmarks to manually superimpose volumes. (new)

    For general Slicer related questions, you can seek help from the online Slicer community through the forum. Please make sure to look at the Frequently Asked Questions about Slicer before posting.

    Where to find 3D specimen data?

    If you are looking for sample 3D specimen data, these repositories are good places to start. Feel free to contact us if you are aware of other large 3D specimen repositories.

    1. MorphSource: MorphoSource is a project-based data archive that allows researchers to store and organize, share, and distribute their own 3d data.
    2. DigiMorph: Digital Morphology library is a dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens.
    3. FaceBase: Comprehensive craniofacial data (including 3D imaging datasets) from model organisms (mouse and zebrafish) and humans.
    4. MorphoBrowser:‘MorphoBrowser’ database and interface is a 3D visualisation and searching tool for mammalian teeth, accessible over the web.
    5. Phenome10K: A free online repository for 3-D scans of biological and palaeontological specimens.
    6. Genetics of craniofacial shape in Mus: High-resolution 3D microCT head scans of a mouse panel between C57BL/6J and A/J mouse strains and associated genotype data. Contains mCT scans of ~500 mice heads and associated cranial landmarks.
    7. Digital Morphology Museum of Kyoto University (KUPRI): DMM provides a large collection of CT and MRI tomography scans of various primates.
    8. The Open Research Scan Archive (formerly: Penn Cranial CT Database) contains high resolution (sub-millimeter) scans of human and non-human crania from the Penn University Museum and other institutions.
    9. MorphoMuseuM (M3): is a peer reviewed, online journal that publishes 3D models of vertebrates, including models of type specimens, anatomy atlases, reconstruction of deformed or damaged specimens, and 3D datasets.
    10. GB3D: Fossils Online project, aims to develop a single database of the type specimens, held in British collections, of macrofossil species and subspecies found in the UK, including links to photographs and a selection of 3D digital models.

    Sample Datasets to test SlicerMorph

    We have couple 3D landmark datasets that you can use to test SlicerMorph. Sample Data can be found at https://github.com/SlicerMorph/SampleData

    Data Dropbox

    We are looking for sample data from diverse set of organisms (and scales) to test our package. It will be greatly helpful, if you can donate sample data for different organisms, and especially for 3D modalities apart from CT/microCT. The public data drop folder is located at https://faculty.washington.edu/maga/data_dropbox/. Please do provide a brief description of the dataset and your e-mail. If you have multiple files (e.g., image stacks, associated landmarks, segmentations, etc.), please zip them as a single file. If you send us any data in proprietary formats (Amira, Avizo, Geomagick, etc.), please provide us with a description of the format so that we can research ways of converting them into an open format correctly and publish the workflow for the benefit of the community.


    For project inquiries or more information please contact SlicerMorph.

    Follow @SlicerMorph

    Funding Acknowledgement

    This project is supported by a NSF Advances in Biological Informatics Collaborative grant to Murat Maga (ABI-1759883), Adam Summers (ABI-1759637) and Doug Boyer (ABI-1759839).