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https://github.com/bluebrain/voxcell

Tools to work with voxel based brain atlases.

https://github.com/bluebrain/voxcell

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    16 of 17 committers (94.1%) from academic institutions
  • ✓
    Institutional organization owner
    Organization bluebrain has institutional domain (portal.bluebrain.epfl.ch)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.6%) to scientific vocabulary

Keywords

atlas build

Keywords from Contributors

neurons morphologies neuroscience biological-simulations computational-neuroscience electrophysiology evolutionary-algorithms genetic-algorithm optimisations parameter
Last synced: 5 months ago · JSON representation

Repository

Tools to work with voxel based brain atlases.

Basic Info
  • Host: GitHub
  • Owner: BlueBrain
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 10.7 MB
Statistics
  • Stars: 5
  • Watchers: 6
  • Forks: 3
  • Open Issues: 4
  • Releases: 9
Archived
Topics
atlas build
Created about 4 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog Contributing License Authors

README.rst 

.. 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/voxcell

Overview
========

This is a library to build circuits and atlases. It contains tools to handle

* "traits fields" and collections and the logic to assign them.
* volumetric data within NRRD files
* Cell collection access / writer.
* to build, transform and handle fields of vectors and orientations.
* querying `Region hierarchy tree`, such as the one available from the `Allen Institute for Brain Science (AIBS)`_: `Mouse Brain Atlas Ontology's StructureGraph`_ (aka 1.json).

Installation
============

Install from PyPI:

.. code-block:: bash

    pip install voxcell

Or an editable install:

.. code-block:: bash

    git clone https://github.com/BlueBrain/voxcell
    cd voxcell
    pip install -e .

Examples
========

To use the following examples, one must download an NRRD file and the Ontology Structure:

.. code-block:: bash

    curl -o brain_regions.nrrd http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_100.nrrd
    curl -o hierarchy.json http://api.brain-map.org/api/v2/structure_graph_download/1.json

One can open NRRD files, and perform operations on them:

.. code-block:: python

    import voxcell
    voxels = voxcell.VoxelData.load_nrrd('brain_regions.nrrd')
    print(voxels.voxel_dimensions)  # prints array([100., 100., 100.], dtype=float32)

One can also use the `Atlas` object to load at both the atlas and the hierarchy:

.. code-block:: python

    import numpy as np
    from voxcell.nexus.voxelbrain import Atlas
    atlas = Atlas.open('.')
    brain_regions = atlas.load_data('brain_regions')
    rm = atlas.load_region_map()
    # count the number of voxels in the VIS region, and all its descendents
    ids = rm.find('VIS', 'acronym', with_descendants=True)
    np.count_nonzero(np.isin(brain_regions.raw, list(ids)))

Citation
========

When you use this software, we kindly ask you to cite the following DOI:

.. image:: https://zenodo.org/badge/451807050.svg
   :target: https://zenodo.org/badge/latestdoi/451807050
   

Acknowledgements
================

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.txt respectively.

Copyright (c) 2022-2024 Blue Brain Project/EPFL

.. _`Allen Institute for Brain Science (AIBS)`: https://alleninstitute.org/what-we-do/brain-science/
.. _`Mouse Brain Atlas Ontology's StructureGraph`: http://api.brain-map.org/api/v2/structure_graph_download/1.json

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

GitHub Events

Total
  • Issues event: 3
  • Delete event: 1
  • Issue comment event: 17
  • Push event: 6
  • Pull request review comment event: 4
  • Pull request review event: 7
  • Pull request event: 6
  • Create event: 1
Last Year
  • Issues event: 3
  • Delete event: 1
  • Issue comment event: 17
  • Push event: 6
  • Pull request review comment event: 4
  • Pull request review event: 7
  • Pull request event: 6
  • Create event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 225
  • Total Committers: 17
  • Avg Commits per committer: 13.235
  • Development Distribution Score (DDS): 0.542
Top Committers
Name Email Commits
Arseny V. Povolotsky a****y@e****h 103
Mike Gevaert m****t@e****h 35
Luis Riquelme l****e@e****h 17
aleksei sanin a****n@e****h 14
lguyot l****t@e****h 11
courcol j****l@e****h 11
tomdele t****x@e****h 10
Gianluca Ficarelli g****i@e****h 6
Benoît Coste b****e@e****h 4
Hugo Thabo Dictus h****s@e****h 3
Liesbeth Vanherpe l****e@e****h 3
Eleftherios Zisis e****s@e****h 2
alex4200 a****z@e****h 2
James Dynes j****s@e****h 1
Adrien Berchet a****t@g****m 1
Christian O'Reilly c****y@e****h 1
antonel stefano s****l@e****h 1
Committer Domains (Top 20 + Academic)
epfl.ch: 16

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 6
  • Total pull requests: 33
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 6
  • Total pull request authors: 8
  • Average comments per issue: 3.83
  • Average comments per pull request: 1.64
  • Merged pull requests: 27
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 3
  • Average time to close issues: 12 days
  • Average time to close pull requests: 2 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 4.0
  • Average comments per pull request: 3.67
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lecriste (1)
  • mgeplf (1)
  • dkeller9 (1)
  • arnaudon (1)
  • seirios (1)
  • ssssarah (1)
Pull Request Authors
  • mgeplf (18)
  • eleftherioszisis (5)
  • adrien-berchet (5)
  • bbpgithubaudit (3)
  • GianlucaFicarelli (3)
  • alex4200 (2)
  • arnaudon (2)
  • edasubert (1)
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 950 last-month
  • Total dependent packages: 2
  • Total dependent repositories: 5
  • Total versions: 11
  • Total maintainers: 3
pypi.org: voxcell

Voxcell is a small library to handle probability distributions that have a spatial component and to use them to build collection of cells in space.

  • Versions: 11
  • Dependent Packages: 2
  • Dependent Repositories: 5
  • Downloads: 950 Last month
Rankings
Dependent repos count: 6.8%
Downloads: 6.9%
Dependent packages count: 7.4%
Average: 12.7%
Forks count: 19.3%
Stargazers count: 23.2%
Maintainers (3)
bbp.opensource mgevaert obi.maintainer
Last synced: 6 months ago

Dependencies

setup.py pypi
  • h5py >=3.1.0
  • numpy >=1.9
  • pandas >=0.24.2
  • pynrrd >=0.4.0
  • requests >=2.18
  • scipy >=1.2.0
.github/workflows/publish-sdist.yml actions
  • actions/checkout master composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/run-tox.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v2 composite
pyproject.toml pypi