Installation¶

Prerequisites¶

Python 3.12 or higher
conda or mamba (recommended)

Standard Installation¶

The recommended user installation is through PyPI:

pip install tad-py

This installs the published version of TAD and its runtime dependencies.

Development Installation¶

If you want to work on TAD locally, clone the repository and install it in editable mode:

git clone https://github.com/Neuro-Interface-Lab/TAD.git
cd TAD
pip install -e ".[dev]"

This installs:

TAD in editable mode
Runtime dependencies such as numpy, matplotlib, spikeinterface, probeinterface, and h5py
Development tools such as pytest, flake8, and documentation dependencies

Installing with conda/mamba¶

The easiest way to install TAD with all dependencies is to use conda:

# Download the environment file
curl -O https://raw.githubusercontent.com/Neuro-Interface-Lab/TAD/main/environment.yml

# Create and activate the environment
conda env create -f environment.yml
conda activate tad-env

This installs:

TAD package in editable mode (-e .)
All runtime dependencies: numpy, matplotlib, spikeinterface, probeinterface, h5py
Development tools: pytest, sphinx, black, flake8
Documentation dependencies: myst-parser, furo

Project Context¶

TAD is developed jointly at:

IMS laboratory, University of Bordeaux
Florian Kolbl, Bioelectronics group:
https://www.ims-bordeaux.fr/research-groups/bioelectronics/
Universidade Federal do Parana (UFPR)
Jaderson Polli, Department of Physics:
http://fisica.ufpr.br/pagina_ppgf_english/

The current package is mainly inspired by the analysis strategies presented in:

Pasquale, V., Massobrio, P., Bologna, L. L., Chiappalone, M., & Martinoia, S. (2008). Self-organization and neuronal avalanches in networks of dissociated cortical neurons. Neuroscience, 153(4), 1354-1369.
Bologna, L. L., Pasquale, V., Garofalo, M., Gandolfo, M., Baljon, P. L., Maccione, A., … & Chiappalone, M. (2010). Investigating neuronal activity by SPYCODE multi-channel data analyzer. Neural Networks, 23(6), 685-697.

Verifying Installation¶

To verify that TAD is installed correctly, run:

import tad
from tad import Raster, Triggers, TimeSlot, MCSData
print("Installation successful!")

System Requirements¶

macOS: Intel and Apple Silicon (arm64) supported
Linux: Ubuntu 20.04 or newer
Windows: Not officially tested
Memory: Minimum 2GB RAM (depends on dataset size)

Troubleshooting¶

ImportError: No module named ‘tad’¶

Make sure you installed the package in the active environment:

pip install tad-py

For development, reinstall in editable mode:

pip install -e .

Build errors with spikeinterface¶

This is usually because you need to install build tools. On macOS:

xcode-select --install

On Ubuntu/Linux:

sudo apt-get install build-essential