neurocomplexity 1.2.2

Criticality, transfer entropy, and autonomy analyses for spike-sorted recordings.

neurocomplexity

A Python package for measuring complexity, criticality and information flow in spike-sorted recordings. It started as a private prototype for analysing NetPyNE simulations and has been rewritten to run, instead, on real experimental data: NWB/iloSort/Phy/SpikeInterface output.

What's actually in it

Criticality & dynamics

• criticality — avalanche size and lifetime exponents (alpha_s, alpha_t), the kappa index, the scaling exponent gamma_fit from the size–lifetime regression, and the theoretically-predicted gamma_predicted = (alpha_t - 1) / (alpha_s - 1) for a Sethna (2001) crackling-noise consistency test. The α_t exponent is fit directly to the lifetime distribution P(T), not derived from the regression slope.
• wilting_mr — Wilting & Priesemann (2018) multi-step regression branching ratio, robust to subsampling.
• shape_collapse — Friedman et al. (2012) avalanche shape collapse, with a scale-invariant residual and a bounded continuous optimiser for γ.

Complexity & geometry

• dimensionality — participation ratio on the per-unit correlation matrix.
• manifold — population-state embedding (PCA / UMAP / t-SNE) for the geometry of neural trajectories (Cunningham & Yu 2014, Gallego et al. 2018).
• multiscale_entropy — Costa, Goldberger, Peng (2002) MSE on population-rate series, built on Richman & Moorman (2000) sample entropy.
• lmc_complexity — López-Ruiz, Mancini, Calbet (1995) statistical complexity C = H · D. See docs/complexity_measures.md for when to use LMC vs MSE — they answer different questions.

Information flow

• transfer_entropy — binary Schreiber TE with Miller-Madow correction; significance via inference.test against jitter / ISI-shuffle nulls.
• partial_information — Williams–Beer I_min PID with quantile multi-level discretisation and Miller–Madow bias correction.
• autonomy — VAR-Granger self-predictability index.

Inference

Every analysis works with the unified inference.test(result, rec, surrogate=..., alternative=...) API. Surrogates: jitter (uniform dithering with optional refractory repair), ISI shuffle, and interval shuffle (now validates non-overlap to prevent silent corruption). P-values use the Phipson & Smyth (2010) +1 floor; the two-sided test is the conventional 2 · min(p_greater, p_less) clipped at 1 (robust to skewed null distributions, unlike a mean-centred form). FDR via Benjamini–Hochberg. Confidence intervals via percentile or BC bootstrap.

Visualisation

viz renders every result as a Nature-style figure (editable SVG/TIFF/JPG, Arial 7 pt, no top/right spines, three named palettes). figure_panel composes labelled multi-panel figures with automatic layout. A CLI wraps the whole pipeline so you can run it from a terminal.

Ingestion

NWB, KiloSort/Phy, SpikeInterface. Helpers: add_quality (Bombcell auto-detection, SpikeInterface metrics, threshold-based curation), add_anatomy (Brainglobe lookups, CSV, SHARP-Track .mat), add_trials (CSV/TSV/NWB), merge_probes (multi-probe sessions).

Scope

Primary target: spike-sorted extracellular recordings. Continuous-signal support (LFP / calcium) is provided via neurocomplexity.analysis._continuous for cases where you want to apply the same measure (TE, MSE, stationarity) to a non-spike trace from the same recording — not as a full LFP toolbox. For that, use mne-python or elephant.

Installing

pip install neurocomplexity

Optional extras: pip install neurocomplexity[viz] pulls in matplotlib, [dev] pulls in pytest. There is also a [sim] extra for the legacy NetPyNE simulation side, which most users will not need.

Python 3.10 or newer.

A minimum-effort example

import neurocomplexity as nc

rec = (nc.io.from_nwb("session_715093703.nwb")
         .filter_units(quality=["good"])
         .with_populations(by="brain_area", on_unassigned="drop")
         .crop(3765.6, 4066.9))

crit = nc.analysis.criticality(rec, populations=["VISp"])
print(crit.alpha_s, crit.alpha_t, crit.r_squared)

The recording object is immutable and the builder methods return new recordings, so it is safe to share between threads or reuse without worrying about state.

From the command line

neurocomplexity analyze session.nwb \
    --start 3765.6 --end 4066.9 \
    --target VISp --sources LGd CA1 \
    -o results/session/

That writes a results.json and a set of SVG/TIFF/JPG figures (one composite overview plus five per-analysis panels) into the output directory. If you just want to re-render the figures from a cached run, neurocomplexity figure results.json -o new_figures/ does that without re-loading the NWB.

Reproducibility

Every result carries a ProvenanceRecord with the source path, a BLAKE2b fingerprint of the file (head + tail + filesize), the loader version, and the package version. The CLI dumps all of that into results.json, so a figure can always be traced back to a specific input.

Tutorial

There is a worked tutorial in tutorial/ that walks through loading an Allen Institute NWB file, choosing a spontaneous epoch, and running all five analyses with a paragraph of commentary at each step.

What it's not

It's not a spike sorter. It expects sorted units. It's not a general-purpose information-theory library either — the estimators in here are the ones the package needs internally, with the bias corrections that matter at the sample sizes a single recording gives you, and that's it.

Citation

If this package contributes to a paper, please cite Wilting & Priesemann (2018, Nature Communications) for the branching-ratio estimator, Friedman et al. (2012, PRL) for the shape collapse, and Williams & Beer (2010) for the PID decomposition — those are the methods, and they deserve the credit.

To cite the software itself, see CITATION.cff. It has no DOI yet: the package is not archived on Zenodo, so there is no immutable identifier to cite. Cite the version and repository URL until that lands.

If you are pinning a version for a paper, note that the v1.2.1 artefact on PyPI was published outside CI and cannot be traced to any commit in this repository — see the CHANGELOG. Use v1.2.2 or later, whose release workflow refuses to publish unless the tag and the packaged version agree. You can re-check the provenance of any result set with neurocomplexity verify results.json.

License

MIT.