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Open Meshed Anatomy

Key Investigators

Presenter location: In-person

Project Description

Open Meshed Anatomy (OMA) is a PhD project, in collaboration with the Open Anatomy Project (OAP), aiming to facilitate and improve computational simulations of human body parts using free and open atlases available from OAP. By leveraging these existing segmented and labeled atlases, OMA streamlines the creation of computational grids/meshes for researchers and integrates valuable spatial anatomy information for a better understanding and visualization of simulation results. Similar to OAP’s goals, the project will offer these resources and visualization tools via an open web platform or 3D Slicer, fostering global collaboration and research among the scientific community.


  1. Objective A. Determine the optimal way to assign labels to mesh elements/nodes describing structural names from the atlas.

  2. Objective B. Improve SlicerAtlasEditor functionalities and merge to SlicerOpenAnatomy extension. Refer to Figure 1 and 2.

  3. Objective C. Implement contextual visualisation of results from computational simulations. Refer to Figure 3.

Approach and Plan

Objective A:

  1. What file extension to use (e.g. VTK?) or to use external file.
  2. Labelling via tags for better querying functionalities (Mike Halle’s idea)

Objective B:

  1. Add option to download via URL the different atlas label maps that Open Anatomy Project offers, including its hierarchy structure json files within 3D Slicer or extension.
  2. Fix non-manifold/corrupt labeled voxels in the label map. This will be useful for generating a clean surface mesh for visualization or volumetric meshing. Refer to Figure 2.

Objective C:

  1. Have options to query different computational results based on different anatomy (from atlas). This may be done via tags or using the structure json files. Refer to Figure 3.
  2. Use SlicerCBM as a sample application of this.

Progress and Next Steps

Img1 Img2 Img3


Simplifying Open Anatomy Project's Brain Atlas to ROI Figure 1: Simplifying Open Anatomy Project’s Brain Atlas to ROI using SlicerAtlasEditor

Fixing non-manifold voxels in atlas label map Figure 2: Fixing non-manifold voxels in atlas label map. [1]

Query and visualize simulation results Figure 3: Query and visualize simulation results on ROI

Background and References

The Open Anatomy Project website: https://www.openanatomy.org/.
Open Anatomy Project’s Brain Atlas: https://github.com/mhalle/spl-brain-atlas.
SlicerOpenAnatomy: https://github.com/PerkLab/SlicerOpenAnatomy.
SlicerAtlasEditor: https://github.com/andy9t7/SlicerAtlasEditor.
SlicerCBM: https://github.com/SlicerCBM/SlicerCBM.

[1] S. J. Owen, M. L. Staten, and M. C. Sorensen, “Parallel hexahedral meshing from volume fractions,” Engineering with Computers, vol. 30, no. 3, pp. 301–313, Jul. 2014, doi: 10.1007/s00366-012-0292-8.