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		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		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		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		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		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
example06		example06_place_fields_glm_basis.py	How does a tensor-product B-spline Poisson GLM recover a known 2-D place field, and how do its rate and second-order diagnostics compare to an LGCP?	python examples/paper/example06_place_fields_glm_basis.py	gallery page
example07		example07_spatiotemporal_hawkes_waves.py	Can the Bartlett spectrum and wave-peak detector recover the speed and direction of a known planar wave embedded in a multivariate Hawkes triggering matrix?	python examples/paper/example07_spatiotemporal_hawkes_waves.py	gallery page
example08		example08_real_place_cells.py	Does a B-spline Poisson GLM trained on real hippocampal place cells produce a held-out spatial pair-correlation inside the inhomogeneous global-rank envelope, and a population rescaled-time ACF inside the Bartlett band?	python examples/paper/example08_real_place_cells.py	gallery page

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

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

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

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

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

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

Example 06: 2-D Place-Field Recovery With a B-Spline GLM Basis and an LGCP Comparator

Question: How does a tensor-product B-spline Poisson GLM recover a known 2-D place field, and how do its rate and second-order diagnostics compare to an LGCP?

Run command: python examples/paper/example06_place_fields_glm_basis.py

Expected figure files:

• docs/figures/example06/fig01_true_vs_basis_recovered_rate.png

• docs/figures/example06/fig02_lgcp_glm_credible_band.png

• docs/figures/example06/fig03_pcf_with_global_envelope.png

Example 07: Spatiotemporal Wave Analysis of a Synthetic Planar-Wave Hawkes Adjacency

Question: Can the Bartlett spectrum and wave-peak detector recover the speed and direction of a known planar wave embedded in a multivariate Hawkes triggering matrix?

Run command: python examples/paper/example07_spatiotemporal_hawkes_waves.py

Expected figure files:

• docs/figures/example07/fig01_adjacency_and_positions.png

• docs/figures/example07/fig02_bartlett_spectrum.png

• docs/figures/example07/fig03_detected_peaks_overlay.png

Example 08: Real Place-Cell Encoding-and-Decoding With Held-Out Spatial GoF

Question: Does a B-spline Poisson GLM trained on real hippocampal place cells produce a held-out spatial pair-correlation inside the inhomogeneous global-rank envelope, and a population rescaled-time ACF inside the Bartlett band?

Run command: python examples/paper/example08_real_place_cells.py

Expected figure files:

• docs/figures/example08/fig01_real_place_fields_panel.png

• docs/figures/example08/fig02_decoded_vs_true_position.png

• docs/figures/example08/fig03_pair_correlation_envelope.png

• docs/figures/example08/fig04_rescaled_acf.png

• docs/figures/example08/fig05_velocity_speed_tuning.png

• docs/figures/example08/fig06_decoder_baseline_vs_velocity.png

• docs/figures/example08/fig07_history_kernels.png

• docs/figures/example08/fig08_decoder_baseline_vs_history.png

• docs/figures/example08/fig09_coupling_matrix.png

• docs/figures/example08/fig10_decoder_baseline_vs_progression.png

• docs/figures/example08/fig11_per_cell_lag_ccf.png

• docs/figures/example08/fig12_lag_corrected_comparison.png