README

UltraliserDocumentation

Features

• Reconstruction of optimized and watertight triangular mesh models from input triangular soups.
• Reconstruction of large scale volumetric models from input mesh models (that are not neccessiraly watertight).
• Reconstruction of neuronal mesh models from input morphological skeletons in .SWC and .H5 file formats.
• Reconstruction of astrocytic mesh models from input morphological sksletons in .H5 file format.
• Reconstruction of multi-partitioned vascular mesh models from large scale vascular graphs in .H5 and .VMV file formats.
• Reconstruction of watertight mesh models from input .TIFF stacks.
• Reconstruction of watertight mesh models from input volumes in .NRRD file formats.
• Performing morphological analysis of neuronal and vascular morphologies.
• Performing detailed mesh analysis.

Code

Ultraliser is developed in C++. The code is parallelized based on OpenMP.

Dependencies

• OpenMP, a multi-threading library for parallel processing on multi-core CPUs.
• libTIFF, which gives support for the Tag Image File Format (TIFF), a widely used format for storing image data.
• libhdf5, or the Hierarchical Data Format 5 (HDF5) library for stroring data.

Installation

NeuroMorphoVis can be installed to a user-specified directory from a Unix (Linux or macOSX) terminal. Installation procedures are available in this page.

License

Ultraliser is available to download and use under the GNU General Public License, version 3 (GPL, or “free software”). The code is open sourced with approval from the open sourcing committee and principal coordinators of the Blue Brain Project in March 2021.

Publications

The volume reconstruction algorithms in Ultraliser are based on the following paper.

@article{abdellah2017reconstruction,
  title={Reconstruction and visualization of large-scale volumetric models of neocortical 
  circuits for physically-plausible in silico optical studies},
  author={Abdellah, Marwan and Hernando, Juan and Antille, Nicolas and Eilemann, Stefan and 
  Markram, Henry and Sch{\"u}rmann, Felix},
  journal={BMC bioinformatics},
  volume={18},
  number={10},
  pages={402},
  year={2017},
  publisher={BioMed Central}
}

Acknowledgement & Funding

Ultraliser is developed by the Visualization team at the Blue Brain Project, Ecole Polytechnique Federale de Lausanne (EPFL). Financial support was provided by competitive research funding from King Abdullah University of Science and Technology (KAUST).

Attributions

Contact

For more information on Ultraliser, 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 enquiriries, please contact:

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