├── .gitignore ├── Annotation_new_10_ds222_16bit_isosurf.mat ├── Dockerfile ├── LICENSE ├── MATLAB └── pipeline │ ├── +ccf │ └── getSchema.m │ ├── +ephys │ └── getSchema.m │ ├── +experiment │ └── getSchema.m │ ├── +histology │ └── getSchema.m │ ├── +lab │ └── getSchema.m │ ├── +oralfacial_analysis │ └── getSchema.m │ ├── +tracking │ ├── Calib_Results_stereo.mat │ ├── JawTracking3DSid.m │ ├── Jobs.m │ ├── LickPortTracking3DBot.m │ ├── TongueTracking3DBot.m │ └── getSchema.m │ ├── +utils │ └── stereo_triangulation.m │ ├── Calib_Results_stereo.mat │ ├── README.md │ ├── init.m │ └── populate.m ├── README.md ├── data ├── archive_stage │ └── .empty ├── report_stage │ └── .empty └── rigs │ └── rrig │ └── .empty ├── development └── analysis.py ├── dj_local_conf_template.json ├── doc ├── analysis_library.md ├── data_flow.md ├── developer_setup.md ├── ingestion_instruction.md ├── intro.md ├── petrel_archiving.md ├── pipeline_architecture.md ├── schema │ └── .empty ├── static │ ├── .empty │ ├── map-data-arch.png │ ├── map_workflow_diagram.png │ └── pipeline_architecture │ │ ├── MAP_ingestion_diagram-behavior_ingest.svg │ │ ├── MAP_ingestion_diagram-ephys_ingest.svg │ │ ├── MAP_ingestion_diagram-histology_ingest.svg │ │ ├── MAP_ingestion_diagram-tracking_ingest.svg │ │ ├── behav_ingest_erd.svg │ │ ├── ephys_ingest_erd_1.svg │ │ ├── ephys_ingest_erd_2.svg │ │ ├── ephys_probe_insertion.svg │ │ ├── ephys_unit.svg │ │ ├── experiment_session.svg │ │ ├── hist_ingest_erd.svg │ │ ├── histology_probe_unit.svg │ │ ├── lab_probe.svg │ │ ├── lab_subject.svg │ │ ├── probe_clustering_quality.png │ │ ├── probe_driftmap.png │ │ ├── probe_group_photostim.png │ │ ├── probe_group_psth.png │ │ ├── probe_unit_characteristic.png │ │ ├── project_tracks_plot.png │ │ ├── psth_all.svg │ │ ├── report_all.svg │ │ ├── session_CD.png │ │ ├── session_behav_perf.png │ │ ├── session_tracks_plot.png │ │ ├── tracking_tracking.svg │ │ ├── trk_ingest_erd.svg │ │ ├── unit_unit_behavior.png │ │ └── unit_unit_psth.png └── system_management.md ├── docker-compose.template.yml ├── hexcode.csv ├── images ├── ccf.png ├── ephys.png ├── experiment.png ├── histology.png ├── lab.png ├── plot_avg_contra_ipsi_psth.png ├── plot_clustering_quality.png ├── plot_paired_coding_direction.png ├── plot_psth_bilateral_photostim_effect.png ├── plot_stacked_contra_ipsi_psth.png ├── plot_unit_characteristic.png ├── plot_unit_selectivity.png ├── psth.png ├── publication.png ├── report.png └── tracking.png ├── mousebrainontology_2.csv ├── notebook ├── browse_dandisets.ipynb ├── data-visualization │ ├── behavior and tracking visualization.ipynb │ ├── ephys analysis results visualization.ipynb │ ├── foraging_inspector.ipynb │ └── histology visualization.ipynb ├── data_export.ipynb ├── data_export_nwb.ipynb ├── globus_video_tracking.ipynb ├── new_clustering_comparison.ipynb └── workshop │ ├── 1_data_browsing_demo.ipynb │ ├── 2_visualization_of_ephys_data.ipynb │ └── 3_visualization_of_behavior.ipynb ├── pipeline ├── __init__.py ├── ccf.py ├── ephys.py ├── experiment.py ├── export │ ├── __init__.py │ ├── matlab.py │ └── nwb.py ├── fixes │ ├── __init__.py │ ├── fix_0001_photostim.py │ ├── fix_0002_delay_events.py │ ├── fix_0003_publication_filetype.py │ ├── fix_0004_trial_water_electrode_config_name.py │ ├── fix_0005_earlydelay_latedelay_photostim.py │ ├── fix_0006_delay_duration.py │ ├── fix_0007_amplitude_scaling_for_npx2_probes.py │ ├── fix_0008_ingest_peak_chn_waveform.py │ ├── fix_0009_wf_amp_scaling_for_npx2_probes.py │ ├── fix_0010_spike_sites_and_spike_depths.py │ ├── fix_0011_add_onto_id_and_hexcode.py │ ├── fix_0012_archived_spike_sites_and_spike_depths.py │ ├── fix_0013_waveform_matched_with_metrics.py │ ├── fix_0014_undo_bitvolt_scaling_for_unit_amp.py │ ├── fix_0015_undo_amp_scaling_fix.py │ ├── fix_0016_fix_ccf_electrode_schema.py │ ├── fix_0017_determine_photostim_trial.py │ ├── fix_0018_auto_water.py │ ├── fix_0019_add_missing_photostim_trial.py │ ├── fix_0020_histology_flip.py │ └── fix_history.py ├── foraging_analysis.py ├── foraging_model.py ├── foraging_populate.py ├── globus.py ├── histology.py ├── ingest │ ├── __init__.py │ ├── behavior.py │ ├── ephys.py │ ├── histology.py │ ├── tracking.py │ └── utils │ │ ├── __init__.py │ │ ├── foraging_bpod.py │ │ ├── paths.py │ │ ├── readSGLX.py │ │ └── spike_sorter_loader.py ├── lab.py ├── model │ ├── __init__.py │ ├── bandit_model.py │ ├── bandit_model_comparison.py │ ├── fitting_functions.py │ ├── helper_func.py │ └── util.py ├── mtl_analysis │ ├── ComputePanel.py │ ├── ComputePanelBase.py │ ├── Data.py │ ├── __init__.py │ ├── helper_functions.py │ ├── process_configs.py │ └── utils.py ├── oralfacial_analysis.py ├── plot │ ├── __init__.py │ ├── behavior_plot.py │ ├── foraging_model_plot.py │ ├── foraging_plot.py │ ├── histology_plot.py │ ├── ipython.html │ ├── unit_characteristic_plot.py │ ├── unit_psth.py │ └── util.py ├── psth.py ├── psth_foraging.py ├── publication.py ├── reference │ ├── __init__.py │ └── ccf_ontology.py ├── report.py ├── shell.py ├── tracking.py └── util.py ├── requirements.txt ├── scripts ├── archive_clustering_results_July2022.py ├── delay_response_NWB_export_Nov2022.py ├── globus-shell.py ├── map-mock-data.py └── mapshell.py ├── setup.py ├── test-requirements.txt ├── test_data ├── behavior │ ├── dl25_tw2_20180225_102508.mat │ └── dl25_tw2_20180225_113325.mat ├── dj_local_conf.json.unittest ├── ephys │ └── dl25 │ │ └── 2018-02-25 │ │ └── 1 │ │ ├── dl25_bitcode.mat │ │ └── dl25_g0_t100.imec.ap_imec3_opt3_jrc.mat └── raw │ ├── README │ └── dl25 │ └── 2018-02-25 │ └── 1 │ ├── dl25_2018-02-25_1_g0_t0.imec.ap.bin │ ├── dl25_2018-02-25_1_g0_t0.imec.ap.meta │ ├── dl25_2018-02-25_1_g0_t0.imec.lf.bin │ └── dl25_2018-02-25_1_g0_t0.imec.lf.meta ├── tests ├── test_globus.py └── test_mapshell.py └── workers ├── .env ├── Dockerfile ├── dj_local_conf_template.json └── docker-compose.workers.yml /.gitignore: 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