├── .gitattributes ├── .github └── workflows │ ├── docs_build_and_deploy.yml │ └── lint_test_and_deploy.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── _static │ ├── css │ │ └── custom.css │ ├── dark-logo-gatsby.png │ ├── dark-logo-niu.png │ ├── dark-logo-swc.png │ ├── dark-logo-ucl.png │ ├── dark-wellcome-logo.png │ ├── light-logo-gatsby.png │ ├── light-logo-niu.png │ ├── light-logo-swc.png │ ├── light-logo-ucl.png │ └── light-wellcome-logo.png │ ├── _templates │ ├── footer_end.html │ └── footer_start.html │ ├── api_index.rst │ ├── community │ ├── contributing_guidelines.md │ ├── feature_roadmap.md │ ├── index.md │ └── technical_docs │ ├── conf.py │ ├── environment.yml │ ├── galleries │ ├── get_started │ │ ├── README.rst │ │ └── slow_feature_overview.py │ ├── how_to │ │ ├── 01_preprocess_a_session.py │ │ ├── 02_manage_configs.py │ │ ├── 03_run_in_slurm.py │ │ ├── 04_slow_spike_sorting.py │ │ ├── 05_sync_channel.py │ │ └── README.rst │ └── tutorials │ │ ├── 01_preprocessing_sessions.py │ │ ├── 01a_supported_preprocessing_steps.py │ │ ├── 02_managing_configs.py │ │ ├── 03_running_with_slurm.py │ │ ├── 04_slow_spike_sorting.py │ │ ├── 05_sync_channel.py │ │ └── README.rst │ ├── get_started │ ├── index.md │ ├── installation.md │ ├── output_folder_formats.md │ └── supported_formats.md │ └── index.md ├── pyproject.toml ├── spikewrap ├── __init__.py ├── configs │ ├── _backend │ │ ├── _default_configs │ │ │ ├── neuropixels+kilosort2_5.yaml │ │ │ └── neuropixels+mountainsort5.yaml │ │ └── canon.py │ ├── config_utils.py │ └── hpc.py ├── examples │ ├── example_session.py │ └── example_tiny_data │ │ ├── openephys │ │ ├── README.md │ │ └── rawdata │ │ │ └── sub-001 │ │ │ └── ses-001 │ │ │ └── ephys │ │ │ └── Record Node 104 │ │ │ ├── experiment1 │ │ │ ├── recording1 │ │ │ │ ├── continuous │ │ │ │ │ └── Neuropix-PXI-100.ProbeA-AP │ │ │ │ │ │ ├── continuous.dat │ │ │ │ │ │ ├── sample_numbers.npy │ │ │ │ │ │ └── timestamps.npy │ │ │ │ ├── events │ │ │ │ │ ├── MessageCenter │ │ │ │ │ │ ├── sample_numbers.npy │ │ │ │ │ │ ├── text.npy │ │ │ │ │ │ └── timestamps.npy │ │ │ │ │ └── Neuropix-PXI-100.ProbeA-AP │ │ │ │ │ │ └── TTL │ │ │ │ │ │ ├── full_words.npy │ │ │ │ │ │ ├── sample_numbers.npy │ │ │ │ │ │ ├── states.npy │ │ │ │ │ │ └── timestamps.npy │ │ │ │ ├── structure.oebin │ │ │ │ └── sync_messages.txt │ │ │ └── recording2 │ │ │ │ ├── continuous │ │ │ │ └── Neuropix-PXI-100.ProbeA-AP │ │ │ │ │ ├── continuous.dat │ │ │ │ │ ├── sample_numbers.npy │ │ │ │ │ └── timestamps.npy │ │ │ │ ├── events │ │ │ │ ├── MessageCenter │ │ │ │ │ ├── sample_numbers.npy │ │ │ │ │ ├── text.npy │ │ │ │ │ └── timestamps.npy │ │ │ │ └── Neuropix-PXI-100.ProbeA-AP │ │ │ │ │ └── TTL │ │ │ │ │ ├── full_words.npy │ │ │ │ │ ├── sample_numbers.npy │ │ │ │ │ ├── states.npy │ │ │ │ │ └── timestamps.npy │ │ │ │ ├── structure.oebin │ │ │ │ └── sync_messages.txt │ │ │ └── settings.xml │ │ └── spikeglx │ │ ├── README.md │ │ └── rawdata │ │ └── sub-001 │ │ └── ses-001 │ │ └── ephys │ │ ├── run-001_g0_imec0 │ │ ├── run-001_g0_t0.imec0.ap.bin │ │ └── run-001_g0_t0.imec0.ap.meta │ │ └── run-002_g0_imec0 │ │ ├── run-002_g0_t0.imec0.ap.bin │ │ └── run-002_g0_t0.imec0.ap.meta ├── process │ ├── _loading.py │ └── _preprocessing.py ├── structure │ ├── _preprocess_run.py │ ├── _raw_run.py │ ├── _sorting_run.py │ └── session.py ├── utils │ ├── _checks.py │ ├── _managing_sorters.py │ ├── _slurm.py │ ├── _utils.py │ └── getters.py └── visualise │ └── _visualise.py ├── tests ├── _tests_internal │ ├── README.md │ ├── _test_slurm.py │ └── _test_sorting_internal.py ├── test_data │ ├── README.md │ └── no_probe │ │ ├── README.md │ │ └── rawdata │ │ └── sub-001 │ │ ├── ses-001 │ │ └── ephys │ │ │ └── RecordNode103 │ │ │ └── experiment1 │ │ │ ├── recording1 │ │ │ ├── continuous │ │ │ │ └── File_Reader-100.0 │ │ │ │ │ ├── continuous.dat │ │ │ │ │ ├── synchronized_timestamps.npy │ │ │ │ │ └── timestamps.npy │ │ │ ├── events │ │ │ │ └── Message_Center-904.0 │ │ │ │ │ └── TEXT_group_1 │ │ │ │ │ ├── channels.npy │ │ │ │ │ ├── text.npy │ │ │ │ │ └── timestamps.npy │ │ │ ├── structure.oebin │ │ │ └── sync_messages.txt │ │ │ └── recording2 │ │ │ ├── continuous │ │ │ └── File_Reader-100.0 │ │ │ │ ├── continuous.dat │ │ │ │ ├── synchronized_timestamps.npy │ │ │ │ └── timestamps.npy │ │ │ ├── events │ │ │ └── Message_Center-904.0 │ │ │ │ └── TEXT_group_1 │ │ │ │ ├── channels.npy │ │ │ │ ├── text.npy │ │ │ │ └── timestamps.npy │ │ │ ├── structure.oebin │ │ │ └── sync_messages.txt │ │ └── ses-002 │ │ └── ephys │ │ └── RecordNode105 │ │ └── experiment1 │ │ ├── recording2 │ │ ├── continuous │ │ │ └── File_Reader-100.0 │ │ │ │ ├── continuous.dat │ │ │ │ ├── synchronized_timestamps.npy │ │ │ │ └── timestamps.npy │ │ ├── events │ │ │ └── Message_Center-904.0 │ │ │ │ └── TEXT_group_1 │ │ │ │ ├── channels.npy │ │ │ │ ├── text.npy │ │ │ │ └── timestamps.npy │ │ ├── structure.oebin │ │ └── sync_messages.txt │ │ └── recording3 │ │ ├── continuous │ │ └── File_Reader-100.0 │ │ │ ├── continuous.dat │ │ │ ├── synchronized_timestamps.npy │ │ │ └── timestamps.npy │ │ ├── events │ │ └── Message_Center-904.0 │ │ │ └── TEXT_group_1 │ │ │ ├── channels.npy │ │ │ ├── text.npy │ │ │ └── timestamps.npy │ │ ├── structure.oebin │ │ └── sync_messages.txt └── test_integration │ ├── README.md │ ├── base.py │ ├── test_openephys.py │ ├── test_preprocessing.py │ ├── test_probe.py │ ├── test_sorting.py │ ├── test_spikeglx_run_loading.py │ ├── test_sync.py │ └── test_whiten.py └── tox.ini /.gitattributes: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.github/workflows/docs_build_and_deploy.yml: -------------------------------------------------------------------------------- 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