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.
Project description
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:
pip install voxcell
Or an editable install:
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:
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:
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:
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:
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
File details
Details for the file voxcell-3.1.9.tar.gz
.
File metadata
- Download URL: voxcell-3.1.9.tar.gz
- Upload date:
- Size: 226.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.0.0 CPython/3.12.2
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | f25e7506ee5ee7ace9552c68f8b1ce3e53afc5133b6bfdd2bed1fdd9942a1c30 |
|
MD5 | 5446c2dc322a6a768c9ff510d8a020c6 |
|
BLAKE2b-256 | eb2b739e68ffccfa548121eb8b2578bee84276cf5bddbf4bf31c7baa34b3add3 |