mea-raster-generator 0.1.0

Raster plot and ASDR analysis for Axion Maestro MEA recordings

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

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Supported input files

Extension	Description
.spk	Axion spike file — recommended, no extra parameters needed
.raw	Axion Maestro continuous raw recording (spike detection on-the-fly)
.npz	Pre-parsed spike cache

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Installation

From PyPI (once published)

pip install mea-raster-asdr

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-asdr

Python 3.8+ required.

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Usage

mea-raster-asdr INPUT_FILE [options]

Positional argument

Argument	Description
INPUT_FILE	Path to .spk, .raw, or .npz recording file

Options

Option	Default	Description
--output-dir DIR	auto	Output directory (default: mea_raster_asdr_output/ next to input file)
--wells WELL [WELL ...]	ALL	Wells to analyse, e.g. A1 B2 C3, or ALL
--time-start FLOAT	0	Start of time window in seconds
--time-end FLOAT	0	End of time window in seconds; 0 = full recording
--asdr-thresh INT	50	ASDR threshold spike count (red dashed line)
--combined / --no-combined	on	Save combined raster+histogram figure
--asdr-y-max FLOAT	0	Y-axis maximum for ASDR panels; 0 = autoscale
--dpi INT	300	Figure resolution in DPI
--rec-seconds FLOAT	—	Recording duration in seconds (required for .raw and .npz)
--bin-ms INT	200	ASDR bin width in ms
--thresh-k FLOAT	5.0	Spike threshold multiplier K for MAD thresholding (.raw only)

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

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Output

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

File	Description
<stem>_<well>_raster_histogram.png	Combined raster + ASDR figure
<stem>_<well>_asdr_histogram.png	Standalone ASDR histogram
<stem>_stats.csv	Per-well statistics (spike counts, rates, ISI, bursts)

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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.