py-mea-axion 0.4.0

End-to-end MEA data analysis for Axion Biosystems instruments

py-mea-axion

End-to-end analysis of multi-electrode array (MEA) recordings from Axion Biosystems instruments, in Python.

py-mea-axion reads raw .spk binary files and carries the analysis through spike metrics, burst detection, network-burst detection, and synchrony measurement, all the way to statistical comparisons and publication-ready figures, driven entirely from the command line.

---

Installation

conda create -n mea python=3.11
conda activate mea
pip install py-mea-axion

For development against a local clone:

git clone https://github.com/Molecularbiologyworld/py-mea-axion.git
cd py-mea-axion
pip install -e .

To install the latest commit on master directly from GitHub:

pip install git+https://github.com/Molecularbiologyworld/py-mea-axion.git

Requirements: Python ≥ 3.10, numpy, scipy, pandas, matplotlib, pingouin, statsmodels.

---

Workflow at a glance

The CLI is organised around four phases:

1. mea-axion build processes a folder of .spk files into a single labelled master CSV.
2. mea-axion plot <subcommand> generates figures from the master CSV.
3. mea-axion stats writes a long-format CSV of pairwise condition-comparison results, using the same statistical dispatcher that drives the violin brackets.
4. mea-axion show-layout prints the well-to-condition map encoded in any master CSV.

There are also mea-axion run (single recording, CSVs and figures) and mea-axion summary (single recording, stdout table) for one-off analyses.

---

Filename convention

build requires every .spk file to carry plate and DIV in its name:

<anything>_Plate<N>_DIV<N>.spk

Detection regex (case-insensitive): Plate(\d+)_DIV(\d+). Anything before or after that block is ignored. Files in the input folder that do not match are skipped with a warning.

Filename	Plate	DIV
Plate1_DIV14.spk	1	14
20251002_Plate2_DIV26.spk	2	26
LGI2KD_Plate3_DIV7_recording2.spk	3	7

---

Build a master CSV

You specify the well-to-condition layout once, on the command line:

mea-axion build "data/" --fs-override 12500 \
  --well 1_A1=SCRM,B1,T1,Batch1 \
  --well 1_A2=KD,B1,T1,Batch1 \
  --well 1_B1=SCRM,B1,T2,Batch1 \
  --well 1_B2=KD,B1,T2,Batch1 \
  ... \
  --out master.csv

Each --well entry follows the form <plate>_<well>=<condition>[,B<bio>,T<tech>,<batch>].

• B<n> (biological replicate) and T<n> (technical replicate) are optional.
• The 4th comma-separated value is the batch label (free-form, e.g. Batch1, Plate2).
• Bio rep auto-derives from (plate, well) if not specified.

Output: master.csv (one row per well per DIV, with metric columns plus condition / bio_rep / tech_rep / batch columns) and a sibling master.build.sh containing the command for re-runs.

Re-using a layout

Three ways to avoid retyping the layout for a follow-up build:

# Option 1: re-run the auto-saved script.
bash master.build.sh

# Option 2: pull the layout from an existing master CSV.
mea-axion build "data_v2/" --fs-override 12500 --layout-from master.csv --out master_v2.csv

# Option 3: print the equivalent --well flags to stdout.
mea-axion show-layout master.csv

---

Plot subcommands

mea-axion plot heatmap     master.csv --metric mean_mfr_active_hz --div 21 --out figs/
mea-axion plot trajectory  master.csv --metric mean_mfr_active_hz --out figs/
mea-axion plot timepoint   master.csv --metric mean_mfr_active_hz --div 21 26 33 --out figs/
mea-axion plot pca         master.csv --out figs/
mea-axion plot raster      "recording.spk" --fs-override 12500 --wells A1 --out figs/

Subcommand	Input	What it produces
heatmap	master CSV	4×6 plate grid, one panel per plate, coloured by metric. One PNG per (metric, DIV).
trajectory	master CSV	Mean ± SEM error-bars per condition across DIVs. One PNG per metric.
timepoint	master CSV	Violin and jitter per condition at one DIV, with user-selectable significance brackets. One PNG per (metric, DIV).
pca	master CSV	PCA scatter coloured by condition. One pooled PNG, or one per --div. Optional loadings figure.
raster	.spk file	Burst raster and ASDR histogram for each well.

Common plot flags

Flag	Effect
--metric COL [COL ...]	One or more metric columns. Omit to plot all numeric columns.
--div N [N ...]	Specific time points (timepoint, pca, heatmap).
--div-min N --div-max N	Filter the time range (trajectory, pca).
--filter COL=VAL[,VAL...]	Restrict the input to specific column values. Repeatable; multiple flags AND together. Example: --filter condition=SCRM --filter DIV=14,28.
--group-order GROUP [GROUP ...]	Explicit condition order (default: alphabetical). Listing a subset excludes other groups from the plot.
--color GROUP=#HEX	Colour per condition. Repeatable. Hex codes or matplotlib named colours both work.
--pool	Flatten bio/tech replicate hierarchy and treat every well as independent. Default is hierarchical (collapse tech reps within bio rep before stats).
--figsize W H	Figure size in inches. Default depends on the plot type.
--out DIR	Output directory (auto-created).

Flags specific to plot timepoint (violins)

Flag	Effect
--test {tukey,mannwhitney,kruskal}	Statistical test for the significance brackets. Default tukey (parametric all-pairs Tukey HSD). mannwhitney runs pairwise Mann-Whitney U with Bonferroni correction. kruskal runs Kruskal-Wallis omnibus followed by Dunn's pairwise post-hoc. The choice is yours; the package does not auto-select.
--compare GROUP_A GROUP_B	Restrict significance brackets to specific pairs. Repeatable.
--point-hue COL	Colour individual jitter points by another column (e.g. batch).
--point-color VALUE=#HEX	Per-value colour palette for --point-hue. Repeatable.
--point-shape COL	Use marker shape (in addition to or instead of colour) for individual jitter points. Default markers cycle circle, square, triangle, diamond, etc.
--point-shape-map VALUE=MARKER	Per-value marker for --point-shape. Repeatable. Markers can be matplotlib codes (o, s, ^, ...) or aliases (circle, square, triangle, ...).
--point-size N	Marker area for jitter points. Default 40.
--show-point-legend	Show a legend mapping point colours to --point-hue values. Default hidden.

Flags specific to plot raster

Flag	Effect
--asdr-bin S	ASDR histogram bin width in seconds. Default 0.2.
--time-start S --time-end S	Restrict to a time window in seconds within the recording. Displayed times keep the original timestamps.
--density-color	Colour each spike tick by local spike density (binned at --asdr-bin). Adds a colour bar underneath the raster.
--density-cmap NAME	Matplotlib colour map for --density-color. Default viridis.
--max-isi S --min-spikes N	Burst-detection thresholds for the orange overlay rectangles.

Flags specific to plot pca

Flag	Effect
--loadings	Also save a per-feature PC loadings CSV and a horizontal bar chart of the top contributors to PC1 and PC2.
--top N	Number of top features to show in the loadings figure. Default 10.
--point-shape COL --point-shape-map VALUE=MARKER	Same as for timepoint, useful for indicating biological replicates by marker shape.

Run mea-axion plot <subcommand> --help for the full per-subcommand option list.

Example: a complete violin command

mea-axion plot timepoint master.csv \
  --metric mean_mfr_active_hz burst_freq_avg network_burst_freq mean_sttc \
  --div 21 26 33 \
  --group-order SCRM LGI2_KD4 LGI2_KD5 \
  --color SCRM=green --color LGI2_KD4=lightcoral --color LGI2_KD5=red \
  --point-shape batch --point-shape-map Batch1=circle --point-shape-map Batch2=square --point-shape-map Batch3=triangle \
  --compare LGI2_KD4 SCRM --compare LGI2_KD5 SCRM \
  --test tukey \
  --pool \
  --out figs/timepoint

Pretty axis labels

Axis labels and colour-bar titles render human-readable names (Mean firing rate (Hz) rather than mean_mfr_active_hz). The CLI flag values still use raw column names, which are easier to type.

---

Statistical analyses (mea-axion stats)

Beyond the brackets shown on violin plots, mea-axion stats writes a long-format CSV of pairwise condition-comparison results. Same data, same dispatcher as the violin brackets, just persisted as a tidy table for supplementary materials.

mea-axion stats master.csv \
  --metric mean_mfr_active_hz burst_freq_avg network_burst_freq mean_sttc \
  --div 28 41 \
  --compare LGI2_KD4 SCRM --compare LGI2_KD5 SCRM \
  --test tukey \
  --pool \
  --out stats_summary.csv

The output CSV has one row per (metric, time-point, pair) combination, with columns metric, DIV, test, group_a, group_b, mean_diff, p_adj, significance, n_a, n_b. Sort by metric and DIV in Excel for a clean supplementary table.

The same --test choice (tukey, mannwhitney, kruskal) applies. Significance labels (*, **, ***, ns) match those used in the figures.

---

Single-recording commands

For ad-hoc inspection of one .spk file without going through build:

# Quick per-well summary printed to the terminal (no files written)
mea-axion summary recording.spk --fs-override 12500

# Full pipeline: writes CSVs and figures to results/
mea-axion run recording.spk --out results/ --fs-override 12500

# Restrict to specific wells
mea-axion summary recording.spk --wells A1 B1 C1 --fs-override 12500

# Analyse only a time window
mea-axion run recording.spk --time-start 300 --time-end 600 --out results/ --fs-override 12500

---

Python API

For programmatic use:

from py_mea_axion import MEAExperiment

exp = MEAExperiment(
    "recording.spk",
    metadata="plate_map.csv",   # optional CSV with well_id, condition, DIV, replicate_id
    fs_override=12500,
).run()

exp.spike_metrics      # per-electrode metrics
exp.burst_table        # one row per detected burst
exp.well_summary       # per-well aggregate (27 metrics)
exp.to_csv("results.csv")

exp.plot_heatmap("A1")
exp.plot_raster("A1")
exp.plot_trajectory("mean_mfr_active_hz")

The py_mea_axion.stats module exposes the same statistical functions used by the CLI:

from py_mea_axion.stats import (
    pairwise_test,            # unified dispatcher: tukey / mannwhitney / kruskal
    tukey_hsd_pairwise,       # Tukey HSD only
    compare_conditions,       # auto-dispatch MW (2 groups) or KW (3+ groups)
    longitudinal_model,       # linear mixed-effects with time x group interaction
    compute_icc,              # intraclass correlation
)

---

Note on Axion .spk files

Some recordings lack a BlockVectorHeader (firmware-dependent). When that happens, sampling-rate detection may guess wrong; pass --fs-override explicitly:

mea-axion run recording.spk --fs-override 12500

12500 Hz is the standard rate for Axion CytoView 24-well plates.

---

Running the tests

pip install -e ".[dev]"
pytest

649 tests covering every module: binary parser, burst detection, network-burst detection, synchrony, statistical tests, every viz function, and every CLI subcommand.

---

Citing

If you use py-mea-axion in your research, please cite:

[manuscript in preparation]

---

License

MIT, see LICENSE.