https://github.com/bluebrain/atlas-enhancement
Tools to generate flatmaps of brain atlases & code to add barrel and barrel column annotations to Allen Mouse CCFv3
https://github.com/bluebrain/atlas-enhancement
neuroinformatics neuroscience
Last synced: about 1 year ago
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Tools to generate flatmaps of brain atlases & code to add barrel and barrel column annotations to Allen Mouse CCFv3
- Host: GitHub
- URL: https://github.com/bluebrain/atlas-enhancement
- Owner: BlueBrain
- License: apache-2.0
- Created: 2024-02-06T14:22:49.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-07-04T15:31:04.000Z (almost 2 years ago)
- Last Synced: 2024-11-13T01:03:04.622Z (over 1 year ago)
- Topics: neuroinformatics, neuroscience
- Language: Jupyter Notebook
- Homepage:
- Size: 16.5 MB
- Stars: 2
- Watchers: 2
- Forks: 3
- Open Issues: 1
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Metadata Files:
- Readme: README.md
- License: LICENSE
- Authors: authors.txt
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README
> [!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/atlas-enhancement
# Enhancement of brain atlases with laminar coordinate systems: Flatmaps and barrel column annotations
This code accompanies the manuscript "Enhancement of brain atlases with laminar coordinate systems: Flatmaps and barrel column annotations" by S. Bolaños-Puchet, A. Teska, et al.
Preprint containing full methods and applications availble on [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.08.24.554204).
Accompanying data available on [Zenodo](https://zenodo.org/doi/10.5281/zenodo.8165004).
## Generation of depth and orientation fields
To generate depth and orientation fields, please refer to the documentation of the following repositories:
* [regiodesics](https://github.com/BlueBrain/regiodesics)
* [atlas-direction-vectors](https://github.com/BlueBrain/atlas-direction-vectors)
* [atlas-placement-hints](https://github.com/BlueBrain/atlas-placement-hints/)
## Flatmapping
Complete workflow to generate flatmaps and perform flatmap-based applications, including visualizing 3D datasets in flat space. For more details, please look at the [README](flatmap/README.md) under `flatmap`.
## Annotation of barrels and barrel columns
Code needed to add barrel cortex annotations to the CCFv3 Allen Atlas at 10 $\mu m$ resolution. For more details, please look at the [README](barrel-annotations/README.md) under `barrel-annotations`.
## Citation
If you use the ``atlas-enhancement`` code or method for your research, we ask you to [cite](https://www.biorxiv.org/content/10.1101/2023.08.24.554204):
> Bolaños-Puchet S., Teska A., et al. (2024). Enhancement of brain atlases with laminar coordinate systems: Flatmaps and barrel column annotations. bioRxiv. DOI: 10.1101/2023.08.24.554204
## Funding & Acknowledgments
This project/research 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.
Copyright (c) 2020-2024 Blue Brain Project/EPFL.
## License
This work is licensed under the Apache License, Version 2.0.