GuPPy
Guided Photometry Analysis in Python, a free and open-source FP analysis tool.
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Download Latest Version (.zip)- action.yml
- action.yml
- all_os_versions.txt
- all_python_versions.txt
- assess-file-changes.yml
- auto-publish.yml
- claude.yml
- dailies.yml
- first_and_last_python_versions.txt
- pr-tests.yml
- run-tests.yml
- GuppyLogo.png
- fig1_decomposition.svg
- fig2_decision_tree.svg
- fig1_what_is_cross_correlation.svg
- fig2_lag_mapping.svg
- fig3_normalisation_discards_amplitude.svg
- fig5_timing_consistency.svg
- fig7_no_systematic_relationship.svg
- fig8_across_trials.svg
- heatmap.png
- psth.png
- session_trace.png
- fig1_technique_schematic.png
- fig2_population_summing.svg
- fig3_space_time_landscape.svg
- fig1_response_columns.svg
- fig2_what_405_captures.svg
- fig3_linear_fit_and_correction.svg
- fig4_what_survives.svg
- fig5_control_diagnostic.svg
- fig6_synthetic_fallback.svg
- fig7_calcium_chain.svg
- fig8_decomposition.svg
- fig1_psth_walkthrough.svg
- fig2_session_drift.svg
- fig3_peak_vs_auc.svg
- fig4_peak_latency.svg
- fig5_edge_rejection.svg
- fig6_burst_rejection.svg
- fig1_transient_extraction.svg
- fig2_drift_failure_and_fix.svg
- fig3_threshold_three_regimes.svg
- fig4_two_stage_walkthrough.svg
- fig5_summary_statistics.svg
- fig1_zscore_cross_session.svg
- fig2_baseline_zscore_contrast.svg
- fig3_modified_zscore_robustness.svg
- fig4_cross_session_limitation.svg
- fig5_psth_baseline_vs_standard.svg
- 01_homepage.png
- 02_data_selection.png
- 02_label_stores.png
- 02_parameters.png
- 02b_label_stores_configured.png
- 03_visualization.png
- 04_read_progress.png
- 05_preprocess_progress.png
- 06_psth_progress.png
- combine_data_run_name.png
- combine_data_sessions_selected.png
- compare_parameters_existing_runs.png
- compare_parameters_run_name.png
- covariate_correlations.png
- covariate_label_stores.png
- dandi_asset_browser.png
- dandi_source_selection.png
- export_to_nwb_button.png
- export_to_nwb_progress.png
- group_analysis_card.png
- group_psth_plot.png
- guppy_architecture_dark.svg
- guppy_architecture_light.svg
- import_custom_events.png
- import_custom_events_button.png
- input_metadata.png
- input_metadata_channels.png
- select_artifact_windows.png
- select_artifact_windows_button.png
- tonic_analysis.png
- tonic_analysis_button.png
- tonic_results.png
- visualize_average_results_toggle.png
- architecture.md
- development_environment.md
- index.md
- new_recording_format.md
- testing.md
- artifacts.md
- cross_correlation.md
- fiber_photometry.md
- index.md
- isosbestic_correction.md
- nwb.md
- psth.md
- transient_detection.md
- zscore.md
- analyze-dandi-data.md
- artifact-removal.md
- combine-data.md
- correlate-behavioral-covariates.md
- export-to-nwb.md
- group-analysis.md
- import-custom-events.md
- index.md
- tonic-analysis.md
- glossary.md
- index.md
- outputs.md
- parameters.md
- artifacts_explainer.py
- cross_correlation_explainer.py
- custom_plots_example.py
- fiber_photometry_explainer.py
- isosbestic_explainer.py
- psth_explainer.py
- transient_detection_explainer.py
- zscore_explainer.py
- compare_parameters.md
- custom_plots.md
- first_analysis.md
- index.md
- conf.py
- index.md
- take_screenshots.py
- __init__.py
- artifact_removal.py
- binned_metrics.py
- combine_data.py
- compute_psth.py
- control_channel.py
- control_fit.py
- covariates.py
- cross_correlation.py
- filtering.py
- io_utils.py
- psth_average.py
- psth_peak_and_area.py
- psth_utils.py
- realignment.py
- standard_io.py
- timestamp_correction.py
- tonic.py
- transients.py
- transients_average.py
- z_score.py
- __init__.py
- base_recording_extractor.py
- csv_recording_extractor.py
- dandi_nwb_recording_extractor.py
- detect_acquisition_formats.py
- doric_recording_extractor.py
- npm_recording_extractor.py
- nwb_recording_extractor.py
- tdt_recording_extractor.py
- __init__.py
- artifact_removal.py
- artifact_windows_page.py
- binned_metrics_view.py
- covariate_correlation_view.py
- custom_events_config.py
- dandi_selector.py
- frontend_utils.py
- input_parameters.py
- metadata_selector.py
- nwb_form_style.py
- parameterized_plotter.py
- sidebar.py
- store_labeling_config.py
- store_labeling_instructions.py
- store_labeling_selector.py
- tonic_epochs.py
- transient_peaks.py
- visualization_dashboard.py
- artifacts_removal_replace_nan.png
- control_signal_artifacts.png
- control_signal_artifacts_removal.png
- control_signal_chunk_selection.png
- Input_Parameters.png
- Input_Parameters_GroupAnalysis.png
- Input_Parameters_Individual.png
- repeat_storenames.png
- Storenames_GUI.png
- transients_detection.png
- Visualization_Heatmap.png
- Visualization_PSTH.png
- artifact_view.py
- export_nwb.py
- group_utils.py
- home.py
- import_custom_events.py
- metadata.py
- preprocess.py
- preprocess_view.py
- psth.py
- read_raw_data.py
- save_parameters.py
- select_artifact_windows.py
- step_view.py
- store_labeling.py
- tonic_analysis.py
- transients.py
- transients_view.py
- visualize.py
- _mock_nwb_common.py
- create_mock_nwbfile_ndx_fiber_photometry_v0_1_ndx_events_v0_2.py
- create_mock_nwbfile_ndx_fiber_photometry_v0_2_core_events.py
- create_mock_nwbfile_ndx_fiber_photometry_v0_2_ndx_events_v0_2.py
- create_stubbed_testing_data.py
- environment_ndx_fiber_photometry_v0_1_ndx_events_v0_2.yaml
- environment_ndx_fiber_photometry_v0_2_core_events.yaml
- environment_ndx_fiber_photometry_v0_2_ndx_events_v0_2.yaml
- screenshot_metadata_form.py
- stub_me112_me113_session.py
- summarize_stubbed_testing_data.py
- __init__.py
- api.py
- consistency.py
- covariate_session.py
- mock_recording_extractor.py
- __init__.py
- _hdf5_io.py
- acquisition_format.py
- artifact_windows.py
- custom_events.py
- nwb_io.py
- nwb_metadata.py
- progress.py
- utils.py
- validation.py
- __init__.py
- binned_metrics.py
- covariate_correlation.py
- preprocessing.py
- shading.py
- transients.py
- __init__.py
- app.py
- logging_config.py
- main.py
- runFiberPhotometryAnalysis.ipynb
- Sample_Control_Channel.csv
- Sample_Signal_Channel.csv
- Sample_TTL.csv
- akinesia.csv
- grooming.csv
- Sample_Control_Channel.csv
- Sample_Signal_Channel.csv
- Sample_TTL.csv
- Sample_Control_Channel.csv
- Sample_Signal_Channel.csv
- Sample_TTL.csv
- D2-EPConsole_0039.doric
- 12282020-cfc-pppda7_0000.csv
- BFPD_Acq_0000.doric
- LiCl_0001.doric
- saline_0001.doric
- bl72bl82_12feb2024_fp.csv
- bl72bl82_12feb2024_stimuli.csv
- FiberData415.csv
- FiberData470.csv
- signals.csv
- ttls.csv
- PagCeAVgatFear_14421.csv
- PagCeAVgatFear_1442_ts0.csv
- PagCeAVgatFear_1512_1.csv
- PagCeAVgatFear_1512_ts0.csv
- mock_nwbfile_ndx_fiber_photometry_v0_1_ndx_events_v0_2.nwb
- mock_nwbfile_ndx_fiber_photometry_v0_2_core_events.nwb
- mock_nwbfile_ndx_fiber_photometry_v0_2_ndx_events_v0_2.nwb
- desktop.ini
- OPTO_GEVI_20260416-260416-104323_ME112-ME113-260420-114630.Tbk
- OPTO_GEVI_20260416-260416-104323_ME112-ME113-260420-114630.Tdx
- OPTO_GEVI_20260416-260416-104323_ME112-ME113-260420-114630.tev
- OPTO_GEVI_20260416-260416-104323_ME112-ME113-260420-114630.tin
- OPTO_GEVI_20260416-260416-104323_ME112-ME113-260420-114630.tnt
- OPTO_GEVI_20260416-260416-104323_ME112-ME113-260420-114630.tsq
- StoresListing.txt
- desktop.ini
- Desktop_Photo_048_392-200728-121222.Tbk
- Desktop_Photo_048_392-200728-121222.Tdx
- Desktop_Photo_048_392-200728-121222.tev
- Desktop_Photo_048_392-200728-121222.tin
- Desktop_Photo_048_392-200728-121222.tnt
- Desktop_Photo_048_392-200728-121222.tsq
- StoresListing.txt
- StoresListing_output_1.txt
- Cohort6_Photo_63_207-181030-103332.Tbk
- Cohort6_Photo_63_207-181030-103332.Tdx
- Cohort6_Photo_63_207-181030-103332.tev
- Cohort6_Photo_63_207-181030-103332.tin
- Cohort6_Photo_63_207-181030-103332.tnt
- Cohort6_Photo_63_207-181030-103332.tsq
- desktop.ini
- StoresListing.txt
- StoresListing_output_1.txt
- 99761-170207-161634_Photometry-161823.Tbk
- 99761-170207-161634_Photometry-161823.Tdx
- 99761-170207-161634_Photometry-161823.tev
- 99761-170207-161634_Photometry-161823.tin
- 99761-170207-161634_Photometry-161823.tnt
- 99761-170207-161634_Photometry-161823.tsq
- desktop.ini
- README.md
- __init__.py
- test_consistency_artifact_removal.py
- test_consistency_combined_data.py
- test_consistency_csv.py
- test_consistency_dff.py
- test_consistency_doric.py
- test_consistency_group_analysis.py
- test_consistency_no_isosbestic.py
- test_consistency_npm.py
- test_consistency_tdt.py
- test_consistency_zscore_method.py
- fiber_photometry_metadata_example.yaml
- __init__.py
- conftest.py
- integration_helpers.py
- test_baseline_epoch_fit.py
- test_binned_metrics.py
- test_covariate_correlations.py
- test_export_nwb.py
- test_integration_artifact_removal.py
- test_integration_bin_psth_trials.py
- test_integration_build_event_to_extractor.py
- test_integration_combine_data.py
- test_integration_cross_correlation.py
- test_integration_dandi.py
- test_integration_dff.py
- test_integration_group_analysis.py
- test_integration_home.py
- test_integration_import_custom_events.py
- test_integration_inter_session_mixed_modality.py
- test_integration_intra_session_mixed_modality.py
- test_integration_ndx_events_import_state.py
- test_integration_no_isosbestic.py
- test_integration_npm_params_persistence.py
- test_integration_parallel.py
- test_integration_parametrized_outputs.py
- test_integration_photobleaching_detrend.py
- test_integration_save_parameters.py
- test_integration_spontaneous_mode.py
- test_integration_step1.py
- test_integration_step1_idempotent.py
- test_integration_step2.py
- test_integration_step3.py
- test_integration_step4.py
- test_integration_step5.py
- test_integration_underscore_recording_site.py
- test_integration_zscore_method.py
- test_tonic.py
- __init__.py
- conftest.py
- test_ui_homepage.py
- test_ui_metadata.py
- test_ui_parameter_form.py
- test_ui_sidebar.py
- test_ui_store_labeling.py
- test_ui_visualization.py
- __init__.py
- conftest.py
- test_artifact_removal.py
- test_baseline_epoch_fit.py
- test_binned_metrics.py
- test_combine_data.py
- test_compute_psth.py
- test_control_channel.py
- test_control_fit.py
- test_covariates.py
- test_cross_correlation.py
- test_filtering.py
- test_io_utils.py
- test_psth_average.py
- test_psth_peak_and_area.py
- test_psth_utils.py
- test_standard_io.py
- test_timestamp_correction.py
- test_tonic.py
- test_transients.py
- test_transients_average.py
- test_z_score.py
- __init__.py
- recording_extractor_test_mixin.py
- test_base_recording_extractor.py
- test_csv_recording_extractor.py
- test_dandi_nwb_live.py
- test_dandi_nwb_recording_extractor.py
- test_detect_acquisition_formats.py
- test_doric_recording_extractor.py
- test_npm_recording_extractor.py
- test_nwb_recording_extractor.py
- test_tdt_recording_extractor.py
- __init__.py
- conftest.py
- test_artifact_removal.py
- test_artifact_windows_page.py
- test_binned_metrics_view.py
- test_covariate_correlation_view.py
- test_custom_events_config.py
- test_dandi_selector.py
- test_frontend_utils.py
- test_input_parameters.py
- test_metadata_selector.py
- test_nwb_form_style.py
- test_parameterized_plotter.py
- test_sidebar.py
- test_store_labeling_config.py
- test_store_labeling_instructions.py
- test_store_labeling_selector.py
- test_tonic_epochs.py
- test_transient_peaks.py
- test_visualization_dashboard.py
- __init__.py
- conftest.py
- test_artifact_view.py
- test_export_nwb.py
- test_home.py
- test_import_custom_events.py
- test_metadata.py
- test_preprocess.py
- test_preprocess_view.py
- test_psth.py
- test_read_raw_data.py
- test_save_parameters.py
- test_select_artifact_windows.py
- test_step_view.py
- test_store_labeling.py
- test_tonic_analysis.py
- test_transients.py
- test_transients_view.py
- test_visualize.py
- __init__.py
- test_api.py
- test_consistency.py
- __init__.py
- test_acquisition_format.py
- test_artifact_windows.py
- test_custom_events.py
- test_nwb_io.py
- test_nwb_metadata.py
- test_progress.py
- test_utils.py
- test_validation.py
- __init__.py
- test_binned_metrics.py
- test_covariate_correlation.py
- test_preprocessing.py
- test_shading.py
- test_transients.py
- __init__.py
- test_app.py
- test_main.py
- conftest.py
- guppy_test_data.py
- .coverage
- .gitattributes
- .gitignore
- .pre-commit-config.yaml
- .readthedocs.yaml
- CHANGELOG.md
- codecov.yml
- LICENSE
- MANIFEST.in
- pyproject.toml
- README.md
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