Welcome to SlicerMorph

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 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

For a detailed description of SlicerMorph, see this preprint.

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. Alternatively, you can obtain a custom version of Slicer that's prepackaged with SlicerMorph.

3D Slicer website provides a plethora of documentation.
You can find documentation about SlicerMorph specific modules at SlicerMorph repository
Tutorials from our short courses can also be found here. For use cases that involve high-resolution, non-clinical datasets, you can look at these following tutorials.

  1. A summary SlicerMorph/3D Slicer's Key Modules and Functionality
  2. A detailed example of showcasing existing functionality in 3D Slicer.
  3. Obtaining 3D image stacks from MorphoSource and processing them in 3D Slicer.
  4. How to exchange complex projects with colleagues.
  5. How to import Scanco microCT datasets into 3D Slicer.
  6. Using landmarks to manually superimpose volumes.
  7. How to segment and measure endocranium in Slicer: Comparison of multiple methods
  8. An excellent tutorial by Terrie Simmons-Ehrhardt about how to use MeshLab to edit and merge surface scans

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.

Here are some additional resources for getting started with SlicerMorph

Events

Recurring Online SlicerMorph User Group Meeting

Join us via zoom every 4th Wednesday of the Month at 11 (Seattle)

Upcoming Events

Mid-February 2021 : Tentative Dates for Winter 2021 SlicerMorph Intense Short Course at Friday Harbor. At this point we are waiting to hear from U. Washington about availability of facilities and covid-19 pandemic situation. We expect to make a decision about the workshop by December.

Past Events

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. MorphoSource: MorphoSource is a project-based data archive that allows researchers to store and organize, share, and distribute their own 3d data.
  2. 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.
  3. DigiMorph: Digital Morphology library is a dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens.
  4. FaceBase: Comprehensive craniofacial data (including 3D imaging datasets) from model organisms (mouse and zebrafish) and humans.
  5. MorphoBrowser:‘MorphoBrowser’ database and interface is a 3D visualisation and searching tool for mammalian teeth, accessible over the web.
  6. Phenome10K: A free online repository for 3-D scans of biological and palaeontological specimens.
  7. 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.
  8. Digital Morphology Museum of Kyoto University (KUPRI): DMM provides a large collection of CT and MRI tomography scans of various primates.
  9. 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.
  10. 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.
  11. 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.

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).