├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── LICENSE ├── README.md ├── setup.py └── spiketoolkit ├── __init__.py ├── curation ├── __init__.py └── threshold_metrics.py ├── postprocessing ├── __init__.py ├── features.py ├── postprocessing_tools.py └── utils.py ├── preprocessing ├── __init__.py ├── bandpass_filter.py ├── basepreprocessorrecording.py ├── blank_saturation.py ├── center.py ├── clip.py ├── common_reference.py ├── filterrecording.py ├── highpass_filter.py ├── mask.py ├── normalize_by_quantile.py ├── notch_filter.py ├── preprocessinglist.py ├── rectify.py ├── remove_artifacts.py ├── remove_bad_channels.py ├── resample.py ├── transform.py └── whiten.py ├── sortingcomponents ├── __init__.py └── detection.py ├── tests ├── .gitignore ├── __init__.py ├── test_curation.py ├── test_curation_extractor.py ├── test_postprocessing.py ├── test_preprocessing.py ├── test_sortingcomponents.py ├── test_validation.py └── utils.py ├── utils.py ├── validation ├── __init__.py ├── curation_list.py ├── quality_metric_classes │ ├── __init__.py │ ├── amplitude_cutoff.py │ ├── d_prime.py │ ├── drift_metric.py │ ├── firing_rate.py │ ├── isi_violation.py │ ├── isolation_distance.py │ ├── l_ratio.py │ ├── metric_data.py │ ├── nearest_neighbor.py │ ├── noise_overlap.py │ ├── num_spikes.py │ ├── parameter_dictionaries.py │ ├── presence_ratio.py │ ├── quality_metric.py │ ├── silhouette_score.py │ ├── snr.py │ └── utils │ │ ├── __init__.py │ │ ├── curationsortingextractor.py │ │ ├── thresholdcurator.py │ │ └── validation_tools.py ├── quality_metrics.py └── validation_list.py └── version.py /.github/workflows/python-package.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/.github/workflows/python-package.yml -------------------------------------------------------------------------------- /.github/workflows/python-publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/.github/workflows/python-publish.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/README.md -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/setup.py -------------------------------------------------------------------------------- /spiketoolkit/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/__init__.py -------------------------------------------------------------------------------- /spiketoolkit/curation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/curation/__init__.py -------------------------------------------------------------------------------- /spiketoolkit/curation/threshold_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/curation/threshold_metrics.py -------------------------------------------------------------------------------- /spiketoolkit/postprocessing/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/postprocessing/__init__.py -------------------------------------------------------------------------------- /spiketoolkit/postprocessing/features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/postprocessing/features.py -------------------------------------------------------------------------------- /spiketoolkit/postprocessing/postprocessing_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/postprocessing/postprocessing_tools.py -------------------------------------------------------------------------------- /spiketoolkit/postprocessing/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/postprocessing/utils.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/__init__.py: -------------------------------------------------------------------------------- 1 | from .preprocessinglist import * 2 | -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/bandpass_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/bandpass_filter.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/basepreprocessorrecording.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/basepreprocessorrecording.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/blank_saturation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/blank_saturation.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/center.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/center.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/clip.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/clip.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/common_reference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/common_reference.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/filterrecording.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/filterrecording.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/highpass_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/highpass_filter.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/mask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/mask.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/normalize_by_quantile.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/normalize_by_quantile.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/notch_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/notch_filter.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/preprocessinglist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/preprocessinglist.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/rectify.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/rectify.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/remove_artifacts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/remove_artifacts.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/remove_bad_channels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/remove_bad_channels.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/resample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/resample.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/transform.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/transform.py -------------------------------------------------------------------------------- /spiketoolkit/preprocessing/whiten.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/preprocessing/whiten.py -------------------------------------------------------------------------------- /spiketoolkit/sortingcomponents/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/sortingcomponents/__init__.py -------------------------------------------------------------------------------- /spiketoolkit/sortingcomponents/detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/sortingcomponents/detection.py -------------------------------------------------------------------------------- /spiketoolkit/tests/.gitignore: -------------------------------------------------------------------------------- 1 | phy/ 2 | phy_group/ -------------------------------------------------------------------------------- /spiketoolkit/tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /spiketoolkit/tests/test_curation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/tests/test_curation.py -------------------------------------------------------------------------------- /spiketoolkit/tests/test_curation_extractor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/tests/test_curation_extractor.py -------------------------------------------------------------------------------- /spiketoolkit/tests/test_postprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/tests/test_postprocessing.py -------------------------------------------------------------------------------- /spiketoolkit/tests/test_preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/tests/test_preprocessing.py -------------------------------------------------------------------------------- /spiketoolkit/tests/test_sortingcomponents.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/tests/test_sortingcomponents.py -------------------------------------------------------------------------------- /spiketoolkit/tests/test_validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/tests/test_validation.py -------------------------------------------------------------------------------- /spiketoolkit/tests/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/tests/utils.py -------------------------------------------------------------------------------- /spiketoolkit/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/utils.py -------------------------------------------------------------------------------- /spiketoolkit/validation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/__init__.py -------------------------------------------------------------------------------- /spiketoolkit/validation/curation_list.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/curation_list.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/__init__.py: -------------------------------------------------------------------------------- 1 | from .utils import * 2 | -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/amplitude_cutoff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/amplitude_cutoff.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/d_prime.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/d_prime.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/drift_metric.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/drift_metric.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/firing_rate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/firing_rate.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/isi_violation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/isi_violation.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/isolation_distance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/isolation_distance.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/l_ratio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/l_ratio.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/metric_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/metric_data.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/nearest_neighbor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/nearest_neighbor.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/noise_overlap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/noise_overlap.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/num_spikes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/num_spikes.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/parameter_dictionaries.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/parameter_dictionaries.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/presence_ratio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/presence_ratio.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/quality_metric.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/quality_metric.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/silhouette_score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/silhouette_score.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/snr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/snr.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/utils/curationsortingextractor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/utils/curationsortingextractor.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/utils/thresholdcurator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/utils/thresholdcurator.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metric_classes/utils/validation_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metric_classes/utils/validation_tools.py -------------------------------------------------------------------------------- /spiketoolkit/validation/quality_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/quality_metrics.py -------------------------------------------------------------------------------- /spiketoolkit/validation/validation_list.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SpikeInterface/spiketoolkit/HEAD/spiketoolkit/validation/validation_list.py -------------------------------------------------------------------------------- /spiketoolkit/version.py: -------------------------------------------------------------------------------- 1 | version = '0.7.7' 2 | --------------------------------------------------------------------------------