Science Score: 65.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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✓Institutional organization owner
Organization bluebrain has institutional domain (portal.bluebrain.epfl.ch) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary
Keywords
axon
morphology
neuroscience
neuroscience-methods
Last synced: 6 months ago
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JSON representation
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Repository
A package to synthesize artificial axons
Basic Info
- Host: GitHub
- Owner: BlueBrain
- License: apache-2.0
- Language: Python
- Default Branch: main
- Homepage: https://axon-synthesis.readthedocs.io/
- Size: 20.4 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 7
Topics
axon
morphology
neuroscience
neuroscience-methods
Created over 1 year ago
· Last pushed about 1 year ago
Metadata Files
Readme
Changelog
Contributing
License
Citation
Authors
README.md
Warning
The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization. Future development will take place at: https://github.com/openbraininstitute/axon-synthesis
Axon Synthesis
A package to synthesize artificial axons.
The main documentation, is available here: https://axon-synthesis.readthedocs.io
Installation
It is recommended to install axon-synthesis using pip:
bash
pip install axon-synthesis
Examples
An example can be found in the examples directory.
This example contains a small input dataset and a run.sh script that will execute the code.
The inputs can be reviewed and modified for testing.
Citation
When you use the axon-synthesis software or method for your research, we ask you to cite the
publication associated to this repository (use the Cite this repository button on the
main page of the code).
Funding & Acknowledgment
The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.
For license and authors, see LICENSE.txt and AUTHORS.md respectively.
Copyright © 2023-2024 Blue Brain Project, EPFL
Owner
- Name: The Blue Brain Project
- Login: BlueBrain
- Kind: organization
- Email: bbp.opensource@epfl.ch
- Location: Geneva, Switzerland
- Website: https://portal.bluebrain.epfl.ch/
- Repositories: 226
- Profile: https://github.com/BlueBrain
Open Source Software produced and used by the Blue Brain Project
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: Computational generation of long-range axonal morphologies
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Adrien
family-names: Berchet
email: adrien.berchet@gmail.com
affiliation: 'Blue Brain Project, EPFL'
orcid: 'https://orcid.org/0000-0001-6354-9947'
- family-names: Petkantchin
given-names: Rémy
orcid: 'https://orcid.org/0000-0001-8137-8811'
affiliation: 'Blue Brain Project, EPFL'
email: remy.pet@gmail.com
- given-names: Henry
family-names: Markram
affiliation: 'Blue Brain Project, EPFL'
email: henry.markram@epfl.ch
- given-names: Lida
family-names: Kanari
email: lida.kanari@gmail.com
affiliation: 'Blue Brain Project, EPFL'
orcid: 'https://orcid.org/0000-0002-9539-5070'
identifiers:
- type: doi
value: 10.1101/2024.10.16.618695
description: Preprint on BioRxiv
repository-code: 'https://github.com/BlueBrain/axon-synthesis'
url: 'https://axon-synthesis.readthedocs.io/en/stable/'
abstract: >-
Long-range axons are fundamental to brain connectivity and
functional organization, enabling communication between
different regions of the brain. Recent advances in
experimental techniques have yielded a substantial number
of whole-brain axonal reconstructions. While most previous
computational generative models of neurons have
predominantly focused on dendrites, generating realistic
axonal morphologies is challenging due to their distinct
targeting. In this study, we present a novel algorithm for
axon synthesis that combines algebraic topology with the
Steiner tree algorithm, an extension of the minimum
spanning tree, to generate both the local and long-range
compartments of axons. We demonstrate that our
computationally generated axons closely replicate
experimental data in terms of their morphological
properties. This approach enables the generation of
biologically accurate long-range axons that span large
distances and connect multiple brain regions, advancing
the digital reconstruction of the brain. Ultimately, our
approach opens up new possibilities for large-scale
in-silico simulations, advancing research into brain
function and disorders.
keywords:
- neuronal morphology
- axon synthesis
- Steiner tree
- algebraic topology
- brain connectivity
license: Apache-2.0
GitHub Events
Total
- Create event: 20
- Release event: 6
- Watch event: 1
- Delete event: 17
- Issue comment event: 6
- Member event: 1
- Push event: 21
- Public event: 1
- Pull request event: 29
- Fork event: 1
Last Year
- Create event: 20
- Release event: 6
- Watch event: 1
- Delete event: 17
- Issue comment event: 6
- Member event: 1
- Push event: 21
- Public event: 1
- Pull request event: 29
- Fork event: 1
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 0
- Total pull requests: 21
- Average time to close issues: N/A
- Average time to close pull requests: about 3 hours
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.38
- Merged pull requests: 20
- Bot issues: 0
- Bot pull requests: 2
Past Year
- Issues: 0
- Pull requests: 21
- Average time to close issues: N/A
- Average time to close pull requests: about 3 hours
- Issue authors: 0
- Pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.38
- Merged pull requests: 20
- Bot issues: 0
- Bot pull requests: 2
Top Authors
Issue Authors
- adrien-berchet (1)
Pull Request Authors
- adrien-berchet (24)
- dependabot[bot] (4)
Top Labels
Issue Labels
Pull Request Labels
dependencies (4)
Packages
- Total packages: 1
-
Total downloads:
- pypi 93 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 3
pypi.org: axon-synthesis
A package to synthesize artificial axons
- Homepage: https://axon-synthesis.readthedocs.io
- Documentation: https://axon-synthesis.readthedocs.io/
- License: Apache License 2.0
-
Latest release: 0.1.10
published about 1 year ago
Rankings
Dependent packages count: 10.2%
Average: 33.7%
Dependent repos count: 57.2%
Maintainers (3)
Last synced:
6 months ago
Dependencies
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pypi
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setup.py
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