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
- 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 Tuesday of every month, at 11:00 (PST) online.
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.
- If you used multi-template ALPACA (MALPACA) or kmeans template selection in SlicerMorph, cite the MALPACA this paper in PLOS ONE: Automated landmarking via multiple templates
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:
- Dense Correspondence Analysis (DeCA) for 3D Surfaces: An extension that complements the functionality in SlicerMorph. DeCA integrates anatomical landmarks and 3D surface models into a single workflow which iteratively builds a study template, create dense correspondences and alternatively allow you to generate semiLMs.
- Mouse Embryo Multi-Organ Segmentations (MEMOS): An extension for automated segmentation of contrast-enhanced microCT scans of E15 fetal mouse using deep-learning
- Photogrammetry: An extension to preprocess (mask) large collections of photographs which then can be processed to construct 3D models with texture.
- SlicerMorphR: A convenience library to import and export results from SlicerMorph's GPA module into R.
- ScriptEditor: A simple embedded programming editor for 3D Slicer that allow you to embed your scripts into the Slicer scene and execute directly from it (WIP).
- MorphoDepot: A a git based workflow for sharing and collaborating on segmentation tasks. Ideal for creating classroom project for digital morphology (WIP).
Events
Recurring Online SlicerMorph User Group Meeting
Join us via online every 4th Tuesday of the month at 11PST (please join the mailing list for the meeting link)Upcoming Events
Past Events
- February 10th-13th, 2025 SlicerMorph 102: 3D Morphometrics with SlicerMorph
- January 27th-31st, 2025: 42th NA-MIC Project week. See projects we were involved:
- December 16th-20th, 20243D Digital Morphology and Morphometrics with SlicerMorph at University of Sao Paulo, Brazil
- December 2nd-5th, 2024 SlicerMorph 101: Introduction to 3D Digital Morphology with SlicerMorph
- July 26th, 2024 Introduction to 3D Digital Morphology and Morphometrics with SlicerMorph Full Day Workshop at Evolution 2024. Montreal, QC
- March 22nd, 2024 The Future of Anatomical Visualization: Collaborative Digital Morphology with 3D Slicer and SlicerMorph at Anatomy Connected 2024. Toronto, ON
- Jan 2nd, 2024 Introduction to Digital Morphology with SlicerMorph at the SICB 2024 Annual Meeting, Seattle, WA
- October 2-7, 2023 SlicerMorph Train the Trainers Workshops at the UW Friday Harbor Labs, San Juan Island, WA
- April 19st, 2023 SlicerMorph Workshop at the AABA 2023 Annual Meeting, Reno, NV
- May 22nd, 2023 SlicerMorph Workshops at the TOSCANA 2023 Annual Meeting, Austin, TX
- November 1st, 2022 SlicerMorph Workshop at the SVP 2022 Annual Meeting, Toronto ON
- June 2022: Digital Morphology with SlicerMorph at American Museum of Natural History (in-person)
- May 24-27, 2022: Spring 2022 SlicerMorph Short-Course
- 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.
- March 8-12, 2021: Winter 2021 SlicerMorph Intense Short Course
- 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.
- 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.
- 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 many different datasets to for SlicerMorph tutorials. Primary sample Data can be found at https://github.com/SlicerMorph/SampleData. Others are often referred directly in the tutorial itself.
Data Dropbox
When you are reporting an issue with SlicerMorph, it is often best if you can provide the dataset that you are facing the issue with. Otherwise it gets difficult to replicate the problem on our end. Use this link to upload your data as a zip archive and provide a short description. https://faculty.washington.edu/maga/data_dropbox/.