Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/bluebrain/atlas-direction-vectors

Tools to compute direction vectors in the context of brain atlases.

https://github.com/bluebrain/atlas-direction-vectors

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
    3 of 5 committers (60.0%) from academic institutions
  • ✓
    Institutional organization owner
    Organization bluebrain has institutional domain (portal.bluebrain.epfl.ch)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary

Keywords

atlas build

Keywords from Contributors

neuron
Last synced: 5 months ago · JSON representation

Repository

Tools to compute direction vectors in the context of brain atlases.

Basic Info
  • Host: GitHub
  • Owner: BlueBrain
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 233 KB
Statistics
  • Stars: 3
  • Watchers: 39
  • Forks: 3
  • Open Issues: 4
  • Releases: 5
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/atlas-direction-vectors

|banner|

Overview
=========

This project contains the commands which create direction vectors for several brain regions including the cerebellum, the isocortex, and the thalamus of the AIBS P56 mouse brain.

Direction vectors are 3D unit vectors associated to voxels of a brain region.
They represent the directions of the fiber tracts and their streamlines are assumed to cross transversely layers in laminar brain regions.

Direction vectors are used in placement-algorithm to set cells orientations.

Direction vectors are also used to compute placement hints and split layer 2/3 of the AIBS mouse isocortex.

After installation, you can display the available command lines with the following ``bash`` command:

.. code-block:: bash

    atlas-direction-vectors --help

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

.. code-block:: bash

    pip install atlas-direction-vectors

Examples
========

Direction Vectors
-----------------

Get the required input files:

.. code-block:: bash

   mkdir -p data/ccfv3

   # hierarchy file:
   curl -o data/1.json http://api.brain-map.org/api/v2/structure_graph_download/1.json

   # CCFv3 annotation volume:
   curl -o data/ccfv3/annotation_25.nrrd http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_25.nrrd

Run the code (note, depending on the resolution of the volume, this may require significant amounts of available RAM):

.. code-block:: bash

    atlas-direction-vectors direction-vectors           \
        isocortex                                       \
        --hierarchy-path data/1.json                    \
        --annotation-path data/ccfv3/annotation_25.nrrd \
        --algorithm shading-blur-gradient               \
        --output-path data/ccfv3/direction_vectors.nrrd

For the placeholder orientations, one can compute the vectors for a particular
region with:

.. code-block:: bash

    atlas-direction-vectors direction-vectors           \
    from-center                                         \
        --region SSp                                    \
        --hierarchy-path data/1.json                    \
        --annotation-path data/ccfv3/annotation_25.nrrd \
        --output-path placeholder-direction_vectors.nrrd

Instructions for developers
===========================

Run the following commands before submitting your code for review:

.. code-block:: bash

    cd atlas-direction-vectors
    isort -l 100 --profile black atlas_direction_vectors tests setup.py
    black -l 100 atlas_direction_vectors tests setup.py

These formatting operations will help you pass the linting check `testenv:lint` defined in `tox.ini`.

Citation
========

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

.. image:: https://zenodo.org/badge/451806460.svg
   :target: https://zenodo.org/badge/latestdoi/451806460

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 © 2022-2024 Blue Brain Project/EPFL

.. substitutions

.. |banner| image:: doc/source/static/atlas-direction-vectors.jpg

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
  • Push event: 1
  • Fork event: 1
Last Year
  • Push event: 1
  • Fork event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 18
  • Total Committers: 5
  • Avg Commits per committer: 3.6
  • Development Distribution Score (DDS): 0.278
Top Committers
Name Email Commits
MikeG m****t@e****h 13
Luc Guyot l****t@e****h 2
alex4200 a****z@e****h 1
Dimitri RODARIE d****e@g****m 1
Eduard Šubert 6****t@u****m 1
Committer Domains (Top 20 + Academic)
epfl.ch: 3

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 27
  • Average time to close issues: 7 days
  • Average time to close pull requests: 17 days
  • Total issue authors: 1
  • Total pull request authors: 8
  • Average comments per issue: 1.5
  • Average comments per pull request: 2.11
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • lecriste (2)
Pull Request Authors
  • mgeplf (16)
  • arnaudon (7)
  • asoplata (4)
  • bbpgithubaudit (3)
  • drodarie (2)
  • alex4200 (1)
  • matz-e (1)
  • edasubert (1)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 29 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 6
  • Total maintainers: 2
pypi.org: atlas-direction-vectors

Commands to compute direction vectors in volumetric brain regions. Direction vectors are 3D unit vectors associated to voxels of a brain region. They represent the directions of the fiber tracts.

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 29 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 19.1%
Average: 21.1%
Dependent repos count: 21.5%
Stargazers count: 25.1%
Downloads: 29.5%
Maintainers (2)
bbp.opensource obi.maintainer
Last synced: 6 months ago

Dependencies

setup.py pypi
  • atlas-commons >=0.1.4
  • click >=7.0
  • numpy >=1.15.0
  • numpy-quaternion *
.github/workflows/publish-sdist.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • pypa/gh-action-pypi-publish master composite
.github/workflows/run-tox.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • codecov/codecov-action v2 composite