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nSTAT Paper Examples

This page maps the standalone MATLAB paper examples to the canonical source files and generated outputs in this repository.

Canonical source files:

  • helpfiles/nSTATPaperExamples.mlx
  • helpfiles/nSTATPaperExamples.m

Paper reference:

  • Cajigas I, Malik WQ, Brown EN. nSTAT: Open-source neural spike train analysis toolbox for Matlab. Journal of Neuroscience Methods 211:245-264 (2012). DOI: 10.1016/j.jneumeth.2012.08.009
  • Public article page (captions/section text used for mapping): PMC3491120

Run Everything

From a fresh clone (MATLAB R2025b):

cd('/path/to/nSTAT')
addpath(genpath(pwd));
nSTAT_Install('DownloadExampleData',true);
build_paper_examples;

Outputs:

  • Figures: docs/figures/example01/ ... docs/figures/example05/
  • Manifest: docs/figures/manifest.json

Data and Reproducibility Policy

  • RNG is fixed with rng(0,'twister') in each standalone example.
  • Figures are exported with fixed dimensions and DPI via nstat.docs.exportFigure.
  • The paper-example dataset is not versioned in Git.
  • nSTAT_Install can prompt to download the figshare archive into data/.
  • Noninteractive install:
nSTAT_Install('DownloadExampleData',true)

Example Index

ID Standalone source Primary paper mapping Figure gallery
example01 examples/paper/example01_mepsc_poisson.m Section 2.3.1; mEPSC analyses (related to Figs. 3 and 10) docs/figures/example01
example02 examples/paper/example02_whisker_stimulus_thalamus.m Section 2.3.2; explicit stimulus + history effects (related to Figs. 4 and 11) docs/figures/example02
example03 examples/paper/example03_psth_and_ssglm.m Sections 2.3.3-2.3.4; PSTH and SSGLM (related to Figs. 5, 6, and 12) docs/figures/example03
example04 examples/paper/example04_place_cells_continuous_stimulus.m Section 2.3.5; place-cell receptive fields (related to Figs. 7 and 13) docs/figures/example04
example05 examples/paper/example05_decoding_ppaf_pphf.m Sections 2.3.6-2.3.7; decoding with PPAF/PPHF (related to Figs. 8, 9, 14, plus canonical hybrid extension) docs/figures/example05

Gallery

Example 01: mEPSC Poisson Models

Question: does Mg2+ washout produce firing-rate dynamics beyond a constant Poisson baseline?

Example 01

Example 02: Explicit Stimulus + History (Thalamus)

Question: what stimulus lag and history order best explain whisker-evoked spike trains?

Example 02

Example 03: PSTH and SSGLM

Question: how do PSTH and state-space GLM differ in capturing trial learning dynamics?

Example 03

Example 04: Place-Cell Receptive Fields

Question: how do Gaussian and Zernike basis models compare for place-field mapping across cells and animals?

Example 04

Example 05: Decoding With PPAF and PPHF

Question: how accurately can neural populations decode stimulus/reach state with adaptive and hybrid point-process filters?

Example 05