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marwan-abdellah edited this page Oct 1, 2021 · 7 revisions

Introduction

VessMorphoVis is an integrated suite of toolboxes for interactive visualization and analysis of large brain vascular networks represented by morphological graphs segmented from imaging or microscopy stacks. The workflow leverages the outstanding potentials of Blender, aiming to establish an integrated, extensible and domain-specific framework capable of interactive visualization, analysis, high fidelity meshing and high quality rendering of vascular morphologies.

Features

  • Interactive visualization, analysis and automated repair of large-scale vasculature morphology skeletons.
  • Sketching and building three-dimensional representations of the vascular morphology skeletons using various methods for visual analytics.
  • Automated analysis of neuronal morphology skeletons that are digitally reconstructed from optical microscopy stacks.
  • An easy context to load broken morphology skeletons and repair them manually.
  • Automated reconstruction of polygonal mesh models that represent the surface of the vasvular morphologies based on the piecewise meshing method presented by Abdellah et al., 2017.
  • Accurate mesh reconstruction with meta balls to create watertight meshes for reaction-diffusion simulations.
  • Exporting the reconstructed meshes in several file formats including PLY, OBJ, STL and also as a Blender file (.blend).

Package Details

VessMorphoVis is mainly based on Blender. Blender is a free software and can be downloaded from Blender.org. Blender is released under the GNU General Public License (GPL, or “free software”). The current version of VessMorphoVis is compatible with the following Blender versions:

VessMorphoVis can be downloaded as a binary archive bundled within Blender that can be easily extracted and used out-of-the-box. The optional dependencies are already shiped within this archive using pip on each respective platform. This package (released every minor version update of the software) is recommended for Windows users or those who cannot use the Terminal. Otherwise, users can just download an installation script that will automatically install the entire package to a user-specified directory. This script does not require sudo permissions.

Known Bugs or Feature Requests

Please refer to the github issue tracker for fixed and open bugs. User can also report any bugs and request new features needed for their research. We are happy to provide direct support .

Publications & Citation

If you use VessMorphoVis for your research, media design or other purposes, please cite our paper Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis using the following entry:

@article{abdellah2020interactive,
  title={Interactive visualization and analysis of morphological skeletons 
    of brain vasculature networks with VessMorphoVis},
  author={Abdellah, Marwan and Guerrero, Nadir Román abd Lapere, Samule and 
    Coggan, Jay S. and Coste, Benoit and Dagaer, Snigdha and Keller, Daniel 
    and Courcol, Jean-Denis and Markram, Henry and Sch{\"u}rmann, Felix},
  journal={Bioinformatics},
  volume={In press},
  year={2020},
  publisher={Oxford University Press}
}

Contact

For more information on VessMorphoVis, comments or suggestions, please contact:

Marwan Abdellah
Scientific Visualiation Engineer
Blue Brain Project
marwan.abdellah@epfl.ch

Felix Schürmann
Co-director of the Blue Brain Project
felix.schuermann@epfl.ch

Should you have any questions concerning press enquiries, please contact:

Kate Mullins
Communications
Blue Brain Project
kate.mullins@epfl.ch

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