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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

Science Score: 57.0%

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    Organization bluebrain has institutional domain (portal.bluebrain.epfl.ch)
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Keywords

neuroinformatics neuroscience
Last synced: 6 months ago · JSON representation

Repository

Tools to generate flatmaps of brain atlases & code to add barrel and barrel column annotations to Allen Mouse CCFv3

Basic Info
  • Host: GitHub
  • Owner: BlueBrain
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage:
  • Size: 16.5 MB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 4
  • Open Issues: 1
  • Releases: 0
Archived
Topics
neuroinformatics neuroscience
Created about 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License 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/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.

Accompanying data available on Zenodo.

Generation of depth and orientation fields

To generate depth and orientation fields, please refer to the documentation of the following repositories:

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 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 under barrel-annotations.

Citation

If you use the atlas-enhancement code or method for your research, we ask you to cite:

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.

Owner

  • Name: The Blue Brain Project
  • Login: BlueBrain
  • Kind: organization
  • Email: bbp.opensource@epfl.ch
  • Location: Geneva, Switzerland

Open Source Software produced and used by the Blue Brain Project

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dependencies (1)

Dependencies

requirements.txt pypi
  • Shapely ==2.0.2
  • atlas_splitter ==0.1.2.dev30
  • blueetl ==0.4.0
  • cmcrameri ==1.8
  • colorcet ==3.0.1
  • datashader ==0.16.0
  • hexalattice ==1.3.0
  • joblib ==1.3.2
  • lmfit ==1.2.2
  • matplotlib ==3.7.0
  • numpy ==1.24.2
  • pandas ==1.5.3
  • scikit-spatial ==7.2.0
  • scipy ==1.12.0
  • seaborn ==0.13.2
  • tqdm ==4.64.1
  • voxcell ==3.1.3
  • xarray ==2023.2.0