braian 1.0.5

A python library for easy navigation, visualisation, and analysis of whole-brain quantification data.

BraiAn

Installation

Once you are in an active python>=3.11,<3.14 environment, you can run:

python3 -m pip install braian

Citing

If you use BraiAn in your work, please cite the paper below, currently in pre-print:

Chiaruttini, N., Castoldi, C. et al. ABBA, a novel tool for whole-brain mapping, reveals brain-wide differences in immediate early genes induction following learning. bioRxiv (2024).
https://doi.org/10.1101/2024.09.06.611625

Building

Prerequisites

• git
• Poetry or venv/conda/pyenv/pyenv-win to manage dependencies.

Windows instructions assume that you configured the PATH and PATHEXT variables with its command-line program location (e.g. git or pip). If you can't/didn't, you can juxtapose the path-to-exectuable to the respective commands (e.g., C:\Python311\python instead of python).
If you don't know how, we recommend using Scoop.

Step 1: clone the repository

git clone https://codeberg.org/SilvaLab/BraiAn.git /path/to/BraiAn

Step 2: install

with Poetry

cd /path/to/BraiAn
poetry install # --with docs, to install documentation dependencies
               # --with dev, to install basic dependencies to work on ipython

Poetry will automatically create a virtual environment in which it installs all the dependencies.
If, instead, you want to manage the environment yourself, Poetry uses the one active during the installation.

with pip

Requires python>=3.11,<3.14.

pip install -e /path/to/BraiAn

Note: installing with pip doesn't assure to install the same version of the dependencies used by developers to run and test braian.