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Overview

This project contains tools to split brain atlas regions and refine annotations accordingly.

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

.. code-block:: bash

atlas-splitter --help

Installation

.. code-block:: bash

pip install atlas-splitter

Examples

To split the layer 2/3 of the AIBS mouse isocortex and save modified hierarchy and annotation files, one performs the following:

Note that the required datasets under data/* can be generated by following the example in atlas-direction-vectors_.

.. code-block:: bash

atlas-splitter split-isocortex-layer-23 \ --hierarchy-path data/1.json \ --annotation-path data/ccfv3/annotation_25.nrrd \ --direction-vectors-path data/ccfv3/direction_vectors.nrrd \ --output-hierarchy-path data/ccfv3/split_hierarchy.json \ --output-annotation-path data/ccfv3/split_annotations.nrrd

To add barrel annotations to the Barrel Cortex and save modified hierarchy and annotation files, one performs the following:

.. code-block:: bash

atlas-splitter split-barrel-columns \ --hierarchy-path data/1.json \ --annotation-path data/ccfv3/annotation_25.nrrd \ --barrels-path data/barrel_positions.feather \ --output-hierarchy-path data/ccfv3/split_hierarchy.json \ --output-annotation-path data/ccfv3/split_annotations.nrrd

Instructions for developers

Run the following commands before submitting your code for review:

.. code-block:: bash

cd atlas-splitter
isort -l 100 --profile black atlas_splitter tests setup.py
black -l 100 atlas_splitter 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/451806666.svg :target: https://zenodo.org/badge/latestdoi/451806666

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

.. _atlas-direction-vectors: https://github.com/BlueBrain/atlas-direction-vectors

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