The toolkit enables biologists to retrieve, visualize, measure, annotate, and perform geometric morphometric analyses from high-resolution specimen data both from volumetric scans (CTs and MRs) as well as from 3D surface scanners effectively within 3D Slicer.
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
- Official Slicer Documentation.
- SlicerMorph Module descriptions and documentation
- SlicerMorph Tutorials Repository.
- SlicerMorph Youtube channel that features video tutorials
- SlicerMorph announcements listserv (low volume)
- 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.
- You can also consider attending the monthly user check-in held 4th Wednesday of every month, at 11:00 (PST) online. One time zoom registration is required.
How to Cite SlicerMorph?If you used SlicerMorph in your project, depending on the which module(s) you have interacted with please give citation to one or more of the following papers:
- If you used SlicerMorph for general digital anatomy tasks, or morphometric data collection please cite this paper in Methods in Ecology and Evolution, SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology.
- If you used various semi- and pseudo-landmarking methods implemented in SlicerMorph please cite this paper in American Journal of Physical Anthropology Comparing semi-landmarking approaches for analyzing three-dimensional cranial morphology.
- If you used ALPACA (Automated Landmarking through Pointcloud Alignment and Correspondence Analysis) in SlicerMorph cite the ALPACA paper in Methods in Ecology and Evolution: ALPACA: a fast and accurate computer vision approach for automated landmarking of three-dimensional biological structures.
Some additional tutorials
Recurring Online SlicerMorph User Group MeetingJoin us via zoom every 4th Wednesday of the Month at 11 (Seattle) (one time registration is required)
August 22-29, 2021 SlicerMorph Summer 2021 Intense short-course (tentative dates for in-person event at Friday Harbor Labs)
- June 30, 2021: SlicerMorph demo/workshop for the attendees of The Symposium on Morphometrics and Evolution of Shape (SMEF) 11
- May 26, 2021: ToScA North America 2021 SlicerMorph workshops
- April 2021: Digital Morphology with SlicerMorph at UC Berkeley
- February 11, 2021 : SlicerMorph Workshop for SICB 2021 (full).
- March 8-12, 2021: Winter 2021 SlicerMorph Intense Short
- Jan 2021 SlicerMorph talk presented by Dr. Sara Rolfe at SICB 2021 (needed to be registered to see the talk)
- August 17-21st, 2020 First online SlicerMorph Intense Short Course attended by 75+ participants!
- February 16-23, 2020: Winter 2020 SlicerMorph workshop.
- January 7, 2020: SlicerMorph workshop at the SICB2020 Austin, TX
- January 6, 2020: SlicerMorph Poster at the SICB2020 Austin, TX
- August 26-September 1, 2020: First SlicerMorph workshop.
- June 18, 2019: SlicerMorph presenting at the 7th IADR Academy, Vancouver, BC.
- March 6, 2019: An online demo of SlicerMorph
- January 2019: 30th NA-MIC Project week. See the projects we were involved:
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.
- MorphoSource: MorphoSource is a project-based data archive that allows researchers to store and organize, share, and distribute their own 3d data.
- New Mexico Decedent Image Database (NMDID): provides researchers with access to whole human body computed tomography (CT) scans and a rich body of associated metadata.
- DigiMorph: Digital Morphology library is a dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens.
- FaceBase: Comprehensive craniofacial data (including 3D imaging datasets) from model organisms (mouse and zebrafish) and humans.
- MorphoBrowser:‘MorphoBrowser’ database and interface is a 3D visualisation and searching tool for mammalian teeth, accessible over the web.
- Phenome10K: A free online repository for 3-D scans of biological and palaeontological specimens.
- 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.
- Digital Morphology Museum of Kyoto University (KUPRI): DMM provides a large collection of CT and MRI tomography scans of various primates.
- 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.
- 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.
- 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
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.