mea-raster-asdr

Python tool for analysing multielectrode array (MEA) recordings from the Axion Maestro system.

Generates per-well figures matching the output of the MATLAB pipeline (Axion_TVAloopv3 / v4):

• Top panel — ASDR histogram (spike counts per 200 ms bin, summed across all 16 electrodes)
• Lower rows — Raster plot (one row per electrode, vertical tick per spike)
• Standalone ASDR PNG and statistics CSV also saved

Supported input files

Installation

From PyPI

pip install mea-raster-generator

Local install (from cloned repo)

pip install .

Inside a conda environment

conda create -n mea python=3.10
conda activate mea
pip install mea-raster-generator

Python 3.8+ required.

Usage

mea-raster-asdr INPUT_FILE [options]

Positional argument

Options

Examples

# Analyse well D1 from an .spk file, time window 0–420 s
mea-raster-asdr recording.spk --wells D1 --time-end 420 --asdr-thresh 50

# Analyse all wells, autoscale Y axis
mea-raster-asdr recording.spk --wells ALL --time-end 600

# Raw file (rec-seconds required), save to custom output directory
mea-raster-asdr recording.raw --rec-seconds 360 --wells A1 B1 --output-dir ./results

# ASDR histogram only (no raster)
mea-raster-asdr recording.spk --wells D1 --no-combined

Output

All figures are saved to mea_raster_asdr_output/ next to the input file (or to --output-dir if set):

Background

This tool is a Python port of the MATLAB MEA analysis pipeline developed in the Deane Lab, University of Cambridge. It reads the Axion binary .spk container format based on the official AxIS MATLAB source (AxisFile.m, BlockVectorData.m, etc.) and replicates the spike detection (MAD threshold, identical to MATLAB) and ASDR histogram used in the original pipeline.