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nSTAT Python Paper Examples

This page mirrors the MATLAB paper-example index for the standalone Python port.

Canonical source files:

  • examples/paper/*.py
  • nstat/paper_examples_full.py

Run Everything

python tools/paper_examples/build_gallery.py

Outputs:

  • Figure metadata: docs/figures/manifest.json
  • Gallery page: docs/paper_examples.md
  • Figures: docs/figures/example01/ ... docs/figures/example05/

Example Index

ID Thumbnail Standalone source Question Run command Figure gallery
example01 Example 01 example01_mepsc_poisson.py Do mEPSCs follow constant vs piecewise Poisson firing under Mg2+ washout? python examples/paper/example01_mepsc_poisson.py gallery page
example02 Example 02 example02_whisker_stimulus_thalamus.py How do explicit whisker stimulus and spike history improve thalamic GLM fits? python examples/paper/example02_whisker_stimulus_thalamus.py gallery page
example03 Example 03 example03_psth_and_ssglm.py How do PSTH and SSGLM capture within-trial and across-trial dynamics? python examples/paper/example03_psth_and_ssglm.py gallery page
example04 Example 04 example04_place_cells_continuous_stimulus.py Which receptive-field basis (Gaussian vs Zernike) better fits place cells? python examples/paper/example04_place_cells_continuous_stimulus.py gallery page
example05 Example 05 example05_decoding_ppaf_pphf.py How well do adaptive/hybrid point-process filters decode stimulus and reach state? python examples/paper/example05_decoding_ppaf_pphf.py gallery page 
:hidden:

figures/example01/README
figures/example02/README
figures/example03/README
figures/example04/README
figures/example05/README

Gallery

Example 01: mEPSC Poisson Models Under Constant and Washout Magnesium

Question: Do mEPSCs follow constant vs piecewise Poisson firing under Mg2+ washout?

Run command: python examples/paper/example01_mepsc_poisson.py

Example 01

Expected figure files:

  • docs/figures/example01/fig01_constant_mg_summary.png
  • docs/figures/example01/fig02_washout_raster_overview.png
  • docs/figures/example01/fig03_piecewise_baseline_comparison.png

Example 02: Whisker Stimulus GLM With Lag and History Selection

Question: How do explicit whisker stimulus and spike history improve thalamic GLM fits?

Run command: python examples/paper/example02_whisker_stimulus_thalamus.py

Example 02

Expected figure files:

  • docs/figures/example02/fig01_data_overview.png
  • docs/figures/example02/fig02_lag_and_model_comparison.png

Example 03: PSTH and SSGLM Dynamics Example

Question: How do PSTH and SSGLM capture within-trial and across-trial dynamics?

Run command: python examples/paper/example03_psth_and_ssglm.py

Example 03

Expected figure files:

  • docs/figures/example03/fig01_simulated_and_real_rasters.png
  • docs/figures/example03/fig02_psth_comparison.png
  • docs/figures/example03/fig03_ssglm_simulation_summary.png
  • docs/figures/example03/fig04_ssglm_fit_diagnostics.png
  • docs/figures/example03/fig05_stimulus_effect_surfaces.png
  • docs/figures/example03/fig06_learning_trial_comparison.png

Example 04: Place-Cell Receptive Fields (Gaussian vs Zernike)

Question: Which receptive-field basis (Gaussian vs Zernike) better fits place cells?

Run command: python examples/paper/example04_place_cells_continuous_stimulus.py

Example 04

Expected figure files:

  • docs/figures/example04/fig01_example_cells_path_overlay.png
  • docs/figures/example04/fig02_model_summary_statistics.png
  • docs/figures/example04/fig03_gaussian_place_fields_animal1.png
  • docs/figures/example04/fig04_zernike_place_fields_animal1.png
  • docs/figures/example04/fig05_gaussian_place_fields_animal2.png
  • docs/figures/example04/fig06_zernike_place_fields_animal2.png
  • docs/figures/example04/fig07_example_cell_mesh_comparison.png

Example 05: Stimulus Decoding With PPAF and PPHF

Question: How well do adaptive/hybrid point-process filters decode stimulus and reach state?

Run command: python examples/paper/example05_decoding_ppaf_pphf.py

Example 05

Expected figure files:

  • docs/figures/example05/fig01_univariate_setup.png
  • docs/figures/example05/fig02_univariate_decoding.png
  • docs/figures/example05/fig03_reach_and_population_setup.png
  • docs/figures/example05/fig04_ppaf_goal_vs_free.png
  • docs/figures/example05/fig05_hybrid_setup.png
  • docs/figures/example05/fig06_hybrid_decoding_summary.png