TAD - They All Die¶

TAD logo

TAD is a Python package for handling and analyzing neural spike recordings. It provides tools for spike detection, raster manipulation, burst analysis, synchrony, avalanche analysis, and trigger-based workflows.

Development¶

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/

Scientific Background¶

At this stage, TAD is mainly inspired by the methods and workflows described 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.

Features¶

Flexible Raster Handling: Create, manipulate, and save spike rasters in JSON or HDF5 formats
Spike Metrics: Compute firing rates, spike counts, inter-spike intervals, and more
Avalanche Analysis: Extract and analyze neuronal avalanches
Synchrony Analysis: Compute pairwise neural synchrony
Burst Detection: Detect and characterize burst periods
Flexible Triggers: Define and manage event markers (stimulations, behavioral events)
MCS Data Support: Load and process Multi-Channel Systems recordings

Installation¶

For a standard user installation:

pip install tad-py

For development:

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

Quick Start¶

import numpy as np
from tad import Raster

# Create a raster
raster = Raster.empty(channels=range(10))

# Add spike times
for ch in range(10):
    raster.insert_timestamparray(
        ch, 
        np.random.uniform(0, 10, 100)
    )

# Save to file
raster.save("my_raster.h5", h5=True)

Documentation¶

Installation - Installation and setup
Tutorials - Step-by-step examples
API Reference - Complete API documentation

License¶

TAD is licensed under the GPL-3.0 license. See LICENSE for details.