This is the repository for the SlicerBiomech extension for 3D Slicer.
SlicerBiomech enables the collection and modeling of biomechanical data from 3D specimen data, within the 3D Slicer application.
Notice: The SegmentGeometry extension and module were folded into the SlicerBiomech extension. Install SlicerBiomech to obtain the SegmentGeometry module.
The official method of obtaining SlicerBiomech is through 3D Slicer's built-in Extensions Manager. To obtain SlicerBiomech, first install the most recent stable release of 3D Slicer (currently r31938, 5.4). Use the 3D Slicer Extensions Manager module to search for SlicerBiomech and install the extension. After restarting 3D Slicer, SlicerBiomech modules will be available to use in the application.
Future updates to SlicerBiomech can also be obtained through the Extensions Manager module. To make sure you have the latest version, use the "Check for Updates" button and restart the application.
- SegmentGeometry: Iterates slice-by-slice through a segment to calculate the second moment of area and other cross-sectional properties. Results are exported to a table and plotted for quick visualizations. Inputs are a segmentation node and volume node, but the module can be used to analyze 3D models imported from outside 3D Slicer. Formerly included in the SegmentGeometry extension.
- Dental Dynamics: Uses simple lever mechanics to automate tooth stress calculations for modeling tooth function. Results can be exported and analyzed with the functional homodonty framework.
Learn how to use SlicerBiomech modules through step-by-step tutorials and videos.
If you use SlicerBiomech in your work, please cite one or more relevant publications:
SegmentGeometry
- Huie JM, Summers AP, Kawano SM. (2022) SegmentGeometry: a tool for measuring second moment of area in 3D Slicer. Integrative Organismal Biology 4(1): 1-10. https://doi.org/10.1093/iob/obac009
Dental Dynamics
- Coming Soon
To cite 3D Slicer as a general image analysis platform, please cite:
- Kikinis R, Pieper, SD, Vosburgh KG. (2014) 3D Slicer: A Platform for Subject-Specific Image Analysis, Visualization, and Clinical Support. In Intraoperative Imaging and Image-Guided Therapy (pp. 277–289). Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7657-3_19
The following extensions are automatically installed with SlicerBiomech. Although SlicerBiomech does not directly rely on these extensions, they provide a suite a of tools for importing, visualizing, and segmenting 3D specimen data that are useful for users of SlicerBiomech.
- SlicerMorph: Streamlines digital morphology research by enabling effortless data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data
- SegmentEditorExtraEffects: Provides additional segmentation effects and utilities.
The following extension is used in many workflows for SegmentGeoemtry and Dental Dynamics.
- SurfaceWrapSolidify: A segment editor effect useful for isolating endocasts or filling spaces.
- I received an error or found a bug. What do I do?
Make sure that you have the most recent version of SlicerBiomech by updating the extension. If the error still persists, you can report your issues on the 3D Slicer discourse page and tag me (@jmhuie) or you may email me (jonathanmhuie[at]gmail.com).
- I have a suggestion or feature request for SlicerBiomech. What do I do?
Fantastic! We are always trying to improve the ease and utility of SlicerBiomech modules and would love to hear your suggestions. Please reach out to me through 3D Slicer Discourse page or via email.
Jonathan M. Huie was funded by a NSF Graduate Research Fellowship (DGE-1746914) and a George Washington University Harlan Research Fellowship.