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