Example Index

A visual gallery of the runnable nSTAT examples, mirroring the MATLAB Examples help index. Start with the five paper examples (each a self-contained script with a generated figure gallery), then explore the workflow tutorial notebooks. See also the Paper-Aligned Toolbox Map.

Paper examples

The five canonical examples from Cajigas, Malik & Brown (2012), each reproduced as a standalone Python script. Click a card for its full figure gallery; the Paper Examples page lists every script, run command, and output.

Example 01 mEPSC Poisson models Do mEPSCs follow constant vs piecewise Poisson firing under Mg²⁺ washout? Example 02 Whisker-stimulus GLM Do explicit stimulus and spike history sharpen thalamic GLM fits? Example 03 PSTH and SSGLM dynamics How do PSTH and state-space GLM capture within- and across-trial dynamics? Example 04 Place-cell receptive fields Which basis — Gaussian or Zernike — better fits hippocampal place cells? Example 05 PPAF and PPHF decoding How well do adaptive/hybrid point-process filters decode stimulus and reach state?

By concept — where to start

If you’ve read a Concepts page and want the matching runnable code, this table is the bridge. Tutorial scripts live in examples/tutorials/; the notebooks below are the MATLAB-help ports under notebooks/. New to nSTAT? Start with notebooks/00_getting_started.ipynb — a runnable end-to-end mirror of the 5-minute intro.

Concept page	Tutorial scripts	Notebooks	Paper example
Microelectrode recordings	Tutorial_MicroelectrodeToDecoding.ipynb	00_getting_started, nSpikeTrainExamples	–
Spike trains & GLMs	encoding_to_goodness_of_fit.py, model_comparison.py	AnalysisExamples, HistoryExamples, ExplicitStimulusWhiskerData	Example 02
LFP & spectral analysis	–	SignalObjExamples	–
Goodness-of-fit & decoding	encoding_to_goodness_of_fit.py, decoding_ppaf.py, place_cell_walkthrough.py	DecodingExample, DecodingExampleWithHist, StimulusDecode2D, HippocampalPlaceCellExample	Example 05
State-space & EM	em_dynamax_demo.py	AnalysisExamples2, HybridFilterExample	Example 03
Network connectivity	network_coupling.py	NetworkTutorial	–
Uncertainty & CIs	model_comparison.py	ConfidenceIntervalOverview, FitResSummaryExamples	–
Rhythmic firing & clinical microelectrode	clinical_microelectrode_walkthrough.py, Tutorial_MicroelectrodeToDecoding.ipynb	–	–
Population geometry	place_cell_walkthrough.py (builds population counts)	–	Example 04

Workflow tutorials

Executable notebooks that follow their MATLAB help-page counterparts step for step.

Simulation & example data

PPSimExample Simulate spike trains from a conditional intensity function. PPThinning Generate point-process spike trains by thinning. PSTHEstimation Estimate a peri-stimulus time histogram. ValidationDataSet Reproduce the toolbox validation dataset. mEPSCAnalysis Analyze miniature-EPSC event trains. ExplicitStimulusWhiskerData Explicit-stimulus GLM on thalamic whisker data. HippocampalPlaceCellExample Place-cell receptive fields from position.

Fitting & analysis

AnalysisExamples Fit and assess point-process GLMs. AnalysisExamples2 Further GLM fitting and model selection. ConfidenceIntervalOverview Work with time-varying confidence intervals. TrialExamples Assemble Trial objects from spikes and covariates.

Decoding & networks

DecodingExample Point-process adaptive-filter stimulus decoding. DecodingExampleWithHist Decoding with spike-history covariates. StimulusDecode2D Decode a 2-D stimulus from population spikes. HybridFilterExample Hybrid discrete/continuous point-process filter. NetworkTutorial Functional connectivity via GLM coupling.

Object & class references

Per-class scaffolds that mirror the MATLAB help index method-for-method. These are API reference stubs rather than standalone tutorials — see the Class Definitions and API Reference for the rendered docstrings.

SignalObjExamples CovariateExamples CovCollExamples nSpikeTrainExamples nstCollExamples EventsExamples HistoryExamples TrialConfigExamples ConfigCollExamples FitResultExamples FitResultReference FitResSummaryExamples

Supplementary checks

Small README demos that double as quick install and plotting checks.

Multitaper spectrum & spectrogram python examples/readme_examples/example1_multitaper_and_spectrogram.py Simulated CIF spike train python examples/readme_examples/example2_simulate_cif_spiketrain_10s.py Spike-train raster python examples/readme_examples/example3_nstcoll_raster_from_example2.py