{"id":20956477,"url":"https://github.com/bluebrain/vessmorphovis","last_synced_at":"2025-05-14T05:31:50.265Z","repository":{"id":37544822,"uuid":"211805597","full_name":"BlueBrain/VessMorphoVis","owner":"BlueBrain","description":"A lightweight, interactive, extensible and cross-platform framework for building, visualizing and analyzing vasculature (or blood vessels) morphologies.","archived":false,"fork":false,"pushed_at":"2023-12-19T11:58:51.000Z","size":67210,"stargazers_count":44,"open_issues_count":40,"forks_count":7,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-04-02T13:22:34.444Z","etag":null,"topics":["bbp","blender-addon","blood-vessels","blood-vessels-visualization","blue-brain-project","meshing","morphology","simulation-based-neuroscience","vascular-flow","vascular-networks","visualization"],"latest_commit_sha":null,"homepage":"https://portal.bluebrain.epfl.ch/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BlueBrain.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md"}},"created_at":"2019-09-30T07:51:49.000Z","updated_at":"2024-12-23T11:43:14.000Z","dependencies_parsed_at":"2023-02-06T05:16:03.100Z","dependency_job_id":"fa09e7e5-af86-4435-a82c-aa10dc1b7065","html_url":"https://github.com/BlueBrain/VessMorphoVis","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FVessMorphoVis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FVessMorphoVis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FVessMorphoVis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BlueBrain%2FVessMorphoVis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BlueBrain","download_url":"https://codeload.github.com/BlueBrain/VessMorphoVis/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254076977,"owners_count":22010630,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bbp","blender-addon","blood-vessels","blood-vessels-visualization","blue-brain-project","meshing","morphology","simulation-based-neuroscience","vascular-flow","vascular-networks","visualization"],"created_at":"2024-11-19T01:26:10.357Z","updated_at":"2025-05-14T05:31:47.621Z","avatar_url":"https://github.com/BlueBrain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/DOI/10.1093/bib.btaa461.svg)](https://doi.org/10.1093/bioinformatics/btaa461)\n\n\u003cp align=\"center\"\u003e\n\t\u003cimg src=\"https://raw.githubusercontent.com/wiki/BlueBrain/VessMorphoVis/images/logos/vmv-banner.jpeg\" width=\"1200\"\u003e\n\u003c/p\u003e\n\n# Introduction \n\n_VessMorphoVis_ is an integrated suite of toolboxes for interactive visualization and analysis of \nvast brain vascular networks represented by morphological graphs segmented originally from imaging \nor microscopy stacks. Our workflow leverages the outstanding potentials of Blender, aiming to \nestablish an integrated, extensible and domain-specific framework capable of interactive \nvisualization, analysis, repair, high-fidelity meshing and high-quality rendering of vascular \nmorphologies. _VessMorphoVis_ is developed as an extension to its sister \n[_NeuroMorphoVis_](https://github.com/BlueBrain/NeuroMorphoVis). \n\n## Features\n\n+ Interactive visualization, analysis and automated repair of large-scale vasculature morphology \nskeletons (up to millions of samples).\n\n+ Sketching and building three-dimensional representations of the vascular morphology skeletons \nusing various methods for visual analytics.\n\n+ Analysis of neuronal morphology skeletons that are digitally reconstructed from imaging or \nmicroscopy stacks. \n\n+ An easy context to load broken morphology skeletons and repair them manually. \n\n+ Automated reconstruction of polygonal mesh models that represent the surface of the vasvular \nmorphologies based on the piecewise meshing method presented by \n[Abdellah et al., 2017](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1788-4).\n\n+ Accurate mesh reconstruction with MetaBalls to create watertight meshes for \n[reaction-diffusion simulations](https://en.wikipedia.org/wiki/Reaction%E2%80%93diffusion_system).\n\n+ Large scale and efficient rendering of the vascular morphologies and meshes using the \nWorkbench renderer.\n \n+ Automated high quality rendering of the vascular morphologies and their corresponding meshes \nusing different shading nodes with Cycles.\n\n+ Exporting the reconstructed meshes in several file formats including \n[PLY](https://en.wikipedia.org/wiki/PLY_(file_format)), \n[OBJ](https://en.wikipedia.org/wiki/Wavefront_.obj_file), \n[STL](https://en.wikipedia.org/wiki/STL_(file_format)) \nand also as a Blender file ([.blend](https://en.wikipedia.org/wiki/Blender_(software)#File_format)).\n\n# Package Details\n\n_VessMorphoVis_ is mainly based on [Blender](https://www.blender.org/). \nBlender is a free software and can be downloaded from [Blender.org](http://download.blender.org/release/). \nBlender is released under the GNU General Public License ([GPL](https://www.blender.org/about/license/), or \n“free software”).\nThe current version of _VessMorphoVis_ is compatible with the following Blender versions:\n\n+ [Blender 2.80](http://download.blender.org/release/Blender2.80/)\n+ [Blender 2.81](http://download.blender.org/release/Blender2.81/)\n+ [Blender 2.82](http://download.blender.org/release/Blender2.82/)\n+ [Blender 2.83](http://download.blender.org/release/Blender2.83/)\n\n_VessMorphoVis_ can be downloaded as a __binary archive bundled within Blender__ that can be easily \nextracted and used [out-of-the-box](https://en.wikipedia.org/wiki/Out_of_the_box_(feature)). \nThe optional dependencies are already shiped within this archive using [pip](https://pypi.org/project/pip/) \non each respective platform. This package (released every minor version update of the software) is \nrecommended for __Windows users__ or those who cannot use \nthe [__Terminal__](https://en.wikipedia.org/wiki/Unix_shell). \nOtherwise, users can just download an installation script that will automatically install the entire \npackage to a user-specified directory. This script __does not__ require __sudo__ permissions.\n\n# Documentation \nThe documentation is available [here](https://github.com/BlueBrain/VessMorphoVis/wiki). \n\n# Known Bugs or Feature Requests\n\nPlease refer to the [github issue tracker](https://github.com/BlueBrain/VessMorphoVis/issues) for \nfixed and open bugs. User can also report any bugs and request new features needed for their research. \nWe are happy to provide direct [support](#contact) . \n\n# Gallery \n\n\u003cp align=\"center\"\u003e\n\t\u003cimg src=\"https://github.com/BlueBrain/VessMorphoVis/wiki/images/rendering/BH0031.CNG_artistic.jpg\" width=600\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n\t\u003cimg src=\"https://raw.githubusercontent.com/wiki/BlueBrain/VessMorphoVis/images/rendering/vascular_mesh_column.jpeg\" width=\"600\"\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n\t\u003cimg src=\"https://raw.githubusercontent.com/wiki/BlueBrain/VessMorphoVis/images/rendering/per_segment_coloring_1.jpeg\" height=\"400\"\u003e\n\t\u003cimg src=\"https://raw.githubusercontent.com/wiki/BlueBrain/VessMorphoVis/images/rendering/per_segment_coloring_2.jpeg\" height=\"400\"\u003e\n\u003c/p\u003e\n\n\n# Publications \u0026 Citation \n\nIf you use _VessMorphoVis_ for your research, media design or other purposes, please cite our \npaper _Interactive visualization and analysis of morphological skeletons of brain vasculature \nnetworks with VessMorphoVis_ using the following entry:\n\n```\n@article{abdellah2020interactive,\n  title={Interactive visualization and analysis of morphological skeletons of brain vasculature \n         networks with VessMorphoVis},\n  author={Abdellah, Marwan and Guerrero, Nadir Román abd Lapere, Samule and Coggan, Jay S. and \n          Coste, Benoit and Dagar, Snigdha and Keller, Daniel and Courcol, Jean-Denis and \n          Markram, Henry and Sch{\\\"u}rmann, Felix},\n  journal={Bioinformatics},\n  volume={In press},\n  year={2020},\n  publisher={Oxford University Press}\n}\n```\n\n# Acknowledgement \u0026 Funding\n_VessMorphoVis_ is developed by the Visualization team at the \n[Blue Brain Project](https://bluebrain.epfl.ch/page-52063.html), \n[Ecole Polytechnique Federale de Lausanne (EPFL)](https://www.epfl.ch/). \nThis study was supported by funding to the Blue Brain Project, a research center of the \nÉcole polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the \nSwiss Federal Institutes of Technology.\n\n\n# License \n_VessMorphoVis_ is available to download and use under the GNU General Public License \n([GPL](https://www.gnu.org/licenses/gpl.html), or “free software”). \nThe code is open sourced with approval from the open sourcing committee and principal coordinators \nof the Blue Brain Project in June 2020. \n\nCopyright (c) 2019-2022 Blue Brain Project/EPFL\n\n# Attributions \n\n* [Blender](https://www.blender.org/) (C) is copyright to Blender Foundation. \nThe Blender Foundation is a non-profit organization responsible for the development of Blender. \nBlender is released under the GNU Public License, as Free Software, and therefore can be distributed \nby anyone freely. \n\n* The SWC morphology samples are available from the [Brain Vasculature (BraVa) database](http://cng.gmu.edu/brava). \nThe Brain Vasculature (BraVa) database contains digital reconstructions of the human brain arterial \narborizations from 61 healthy adult subjects along with extracted morphological measurements.\nThe arterial arborizations include the six major trees stemming from the circle of Willis, \nnamely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), \nand Posterior Cerebral Arteries (PCAs). \nCitation: [Susan N. Wright, Peter Kochunov, Fernando Mut Maurizio Bergamino, Kerry M. Brown, John C. Mazziotta, \nArthur W. Toga, Juan R. Cebral, Giorgio A. Ascoli. \nDigital reconstruction and morphometric analysis of human brain arterial vasculature from magnetic \nresonance angiography. NeuroImage, 82, 170-181, (2013)](http://dx.doi.org/10.1016/j.neuroimage.2013.05.089). \n\n* The VMV morphology samples are available with permissions from \n[Pablo Blinder](http://pblab.tau.ac.il/en/), Department of Neurobiology at the Tel Aviv University,\nIsrael. \n\n* The H5 morphology samples are available with permissions from the \n[Blue Brain Project](https://bluebrain.epfl.ch/page-52063.html), \n[Ecole Polytechnique Federale de Lausanne (EPFL)](https://www.epfl.ch/). The original dataset \ncourtesy of [Bruno Weber](https://www.neuroscience.uzh.ch/en/about/people/steering/Weber.html), \nUniversity of Zurich, Switzerland.\n\n* _VessMorphoVis_ depends on the [MorphIO library](https://github.com/BlueBrain/MorphIO) to load \nH5 morphologies. MorphIO is licensed under the terms of the GNU Lesser General Public License \nversion 3.\n\n* The table of contents for all the user documentation pages are generated \nwith [markdown-toc](http://ecotrust-canada.github.io/markdown-toc/).\n \n# Contact\n\nFor more information on _VessMorphoVis_, comments or suggestions, please contact:\n\n__Marwan Abdellah__  \nScientific Visualiation Expert  \nVisualization Team, Computing Division  \nBlue Brain Project  \n[marwan.abdellah@epfl.ch](marwan.abdellah@epfl.ch)  \n[marwan-abdellah.com](http://marwan-abdellah.com)  \n\n\u003cp align=\"center\"\u003e\n\t\u003cimg src=\"https://github.com/BlueBrain/VessMorphoVis/wiki/images/logos/epfl-logo.png\" width=200\u003e\n\u003c/p\u003e\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fvessmorphovis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Fvessmorphovis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Fvessmorphovis/lists"}