Overview

This project contains the common functions used in the context of brain atlases. It is used by the projects:

• https://github.com/BlueBrain/atlas-densities
• https://github.com/BlueBrain/atlas-direction-vectors
• https://github.com/BlueBrain/atlas-placement-hints
• https://github.com/BlueBrain/atlas-splitter

Installation

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

Examples

Create a mask for the region defined by query

from atlas_commons import utils
from voxcell.nexus.voxelbrain import Atlas

# see voxcell documentation for more more information
atlas = Atlas.open('.')
annotation = atlas.load_data('brain_regions')
region_map = atlas.load_region_map()

region = {
    "query": "Isocortex",
    "attribute": "acronym",
    "with_descendants": True,
}
mask = utils.query_region_mask(region, annotation, region_map)

Split input 3D volume into two halves using the middle plane orthogonal to the z-axis

from atlas_commons import utils
import numpy as np

volume = np.array(
    [
        [[0, 1, 2], [2, 3, 4]],
        [[4, 5, 6], [7, 8, 9]],
    ],
    dtype=np.int64,
)
halves = utils.split_into_halves(volume)

Instructions for developers

Run the following commands before submitting your code for review:

cd atlas-commons
isort -l 100 --profile black atlas_commons tests setup.py
black -l 100 atlas_commons tests setup.py

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

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 Blue Brain Project/EPFL