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Open Meshed Anatomy Viewer using Trame Slicer

Key Investigators

• Andy Huynh (University of Western Australia)
• Benjamin Zwick (University of Western Australia)
• Karol Miller (University of Western Australia)
• Adam Wittek (University of Western Australia)

Project Description

The Open Meshed Anatomy Viewer is a web-app for researchers to download and visualize atlas-based meshes/grids for scientific computing based on Trame Slicer. trame-slicer is a Python library bringing 3DSlicer components in trame as a composable library. It uses 3D Slicer’s python wrapping and adds a thin wrapping to make it available with the trame framework.

• The meshes/grids are created from Open Anatomy Project’s SPL/NAC Brain Atlas.
• The Trame Slicer library provides a way for 3D Slicer components to be used in a web-app.

Objective

1. Objective A. Develop a Trame Slicer based web application to view meshes/grid with images.
2. Objective B. Download meshes/grids.
3. Objective C. Host web-app on cloud server.
4. Objective D. Upload simulation results.
5. Objective E. Extract statistics based on anatomical labels.
6. Objective F. Morph meshes/grids to target MRI.

Approach and Plan

1. Create a blank Trame Slicer repo project.
2. Host project on cloud server (e.g. using docker, cap rover etc.).
3. Load images and atlas.
4. Test server-side rendering performance. (related Github Issue).
5. Add features.

Progress and Next Steps

1. We have developed detailed computational meshes using the SPL Brain Atlas.
2. At the 39th Project Week in Montreal (2023) we developed a Trame-based web application that can be used to visualize the Open Meshed Anatomy in 3D Slicer

Illustrations

Background and References

1. Open Meshed Anatomy Project Description - NA-MIC Project Week 39 in Montreal (2023)
2. KitwareMedical/trame-slicer: Bring the capabilities of 3D Slicer to the web with modern UI using the trame framework!