Tools

• Spike Interface
  • Interface with spikeinterface
    • add_recording_to_nwbfile()
    • add_sorting_to_nwbfile()
    • add_devices_to_nwbfile()
    • add_electrodes_to_nwbfile()
    • add_recording_as_time_series_to_nwbfile()
    • add_recording_as_spatial_series_to_nwbfile()
    • add_recording_metadata_to_nwbfile()
    • write_recording_to_nwbfile()
    • write_sorting_to_nwbfile()
    • add_sorting_analyzer_to_nwbfile()
    • write_sorting_analyzer_to_nwbfile()
    • add_recording_as_time_series_to_nwbfile()
    • add_recording_as_spatial_series_to_nwbfile()
  • Data chunk iterator
    • SpikeInterfaceRecordingDataChunkIterator
• ROI extractors
  • Interface with roiextractors
    • get_full_ophys_metadata()
    • add_imaging_to_nwbfile()
    • write_imaging_to_nwbfile()
    • add_segmentation_to_nwbfile()
    • write_segmentation_to_nwbfile()
  • Imaging extractor iterator
    • ImagingExtractorDataChunkIterator
• YAML conversion specification
  • run_conversion_from_yaml()
• NEO
  • get_electrodes_metadata()
  • get_number_of_electrodes()
  • get_number_of_segments()
  • get_command_traces()
  • get_nwb_metadata()
  • add_icephys_electrode()
  • add_icephys_recordings()
  • add_neo_to_nwb()
  • write_neo_to_nwb()
• Testing
  • Data Interface Mixins
    • DataInterfaceTestMixin
    • TemporalAlignmentMixin
    • ImagingExtractorInterfaceTestMixin
    • SegmentationExtractorInterfaceTestMixin
    • RecordingExtractorInterfaceTestMixin
    • SortingExtractorInterfaceTestMixin
    • AudioInterfaceTestMixin
    • VideoInterfaceMixin
    • MedPCInterfaceMixin
    • MiniscopeImagingInterfaceMixin
    • TDTFiberPhotometryInterfaceMixin
    • PoseEstimationInterfaceTestMixin
    • FiberPhotometryInterfaceTestMixin
    • EventsInterfaceTestMixin
  • Mock Interfaces
    • MockInterface
    • MockTimeSeriesInterface
    • MockBehaviorEventInterface
    • MockEventsInterface
    • MockSignalEncodedEventsInterface
    • MockFiberPhotometryInterface
    • MockSpikeGLXNIDQInterface
    • MockRecordingInterface
    • MockSortingInterface
    • MockImagingInterface
    • MockSegmentationInterface
    • MockPoseEstimationInterface
    • MockExternalVideoInterface
    • MockIcephysInterface
  • Mock TTL Signals
    • generate_mock_ttl_signal()
    • regenerate_test_cases()
  • Mock Files
    • generate_path_expander_demo_ibl()
• Iterative Write
  • get_image_series_chunk_shape()
  • get_image_series_buffer_shape()
  • get_electrical_series_chunk_shape()
• Path Expansion
  • AbstractPathExpander
    • AbstractPathExpander.extract_metadata()
    • AbstractPathExpander.list_directory()
    • AbstractPathExpander.expand_paths()
  • LocalPathExpander
    • LocalPathExpander.list_directory()
  • construct_path_template()
• Signal Processing
  • get_rising_frames_from_ttl()
  • get_falling_frames_from_ttl()
• Data Transfers
  • automatic_dandi_upload()
  • get_globus_dataset_content_sizes()
  • transfer_globus_content()
• NWB Helpers
  • BackendConfiguration
    • BackendConfiguration.apply_global_compression()
    • BackendConfiguration.build_remapped_backend()
    • BackendConfiguration.find_locations_requiring_remapping()
    • BackendConfiguration.from_nwbfile()
    • BackendConfiguration.from_nwbfile_with_defaults()
    • BackendConfiguration.from_nwbfile_with_existing()
    • BackendConfiguration.model_config
    • BackendConfiguration.model_json_schema()
    • BackendConfiguration.schema()
    • BackendConfiguration.schema_json()
    • BackendConfiguration.backend
    • BackendConfiguration.pretty_backend_name
    • BackendConfiguration.data_io_class
    • BackendConfiguration.dataset_configurations
  • HDF5BackendConfiguration
    • HDF5BackendConfiguration.backend
    • HDF5BackendConfiguration.data_io_class
    • HDF5BackendConfiguration.model_config
    • HDF5BackendConfiguration.pretty_backend_name
    • HDF5BackendConfiguration.dataset_configurations
  • ZarrBackendConfiguration
    • ZarrBackendConfiguration.backend
    • ZarrBackendConfiguration.data_io_class
    • ZarrBackendConfiguration.model_config
    • ZarrBackendConfiguration.pretty_backend_name
    • ZarrBackendConfiguration.dataset_configurations
    • ZarrBackendConfiguration.number_of_jobs
  • DatasetIOConfiguration
    • DatasetIOConfiguration.compression_method
    • DatasetIOConfiguration.compression_options
    • DatasetIOConfiguration.disk_space_usage_per_chunk_in_bytes
    • DatasetIOConfiguration.from_neurodata_object_with_defaults()
    • DatasetIOConfiguration.from_neurodata_object_with_existing()
    • DatasetIOConfiguration.full_size_in_bytes
    • DatasetIOConfiguration.get_data_io_kwargs()
    • DatasetIOConfiguration.get_dataset()
    • DatasetIOConfiguration.get_kwargs_from_neurodata_object()
    • DatasetIOConfiguration.maximum_ram_usage_per_iteration_in_bytes
    • DatasetIOConfiguration.model_config
    • DatasetIOConfiguration.model_json_schema()
    • DatasetIOConfiguration.model_post_init()
    • DatasetIOConfiguration.schema()
    • DatasetIOConfiguration.schema_json()
    • DatasetIOConfiguration.translate_deprecated_compression_fields()
    • DatasetIOConfiguration.validate_all_shapes()
    • DatasetIOConfiguration.object_id
    • DatasetIOConfiguration.location_in_file
    • DatasetIOConfiguration.dataset_name
    • DatasetIOConfiguration.dtype
    • DatasetIOConfiguration.full_shape
    • DatasetIOConfiguration.chunk_shape
    • DatasetIOConfiguration.buffer_shape
    • DatasetIOConfiguration.compressors
    • DatasetIOConfiguration.compressor_options
  • HDF5DatasetIOConfiguration
    • HDF5DatasetIOConfiguration.from_neurodata_object_with_existing()
    • HDF5DatasetIOConfiguration.get_data_io_kwargs()
    • HDF5DatasetIOConfiguration.model_config
    • HDF5DatasetIOConfiguration.model_post_init()
    • HDF5DatasetIOConfiguration.validate_compressor_order()
    • HDF5DatasetIOConfiguration.compressors
    • HDF5DatasetIOConfiguration.compressor_options
  • ZarrDatasetIOConfiguration
    • ZarrDatasetIOConfiguration.filter_methods
    • ZarrDatasetIOConfiguration.from_neurodata_object_with_existing()
    • ZarrDatasetIOConfiguration.get_data_io_kwargs()
    • ZarrDatasetIOConfiguration.model_config
    • ZarrDatasetIOConfiguration.model_post_init()
    • ZarrDatasetIOConfiguration.translate_deprecated_filter_methods()
    • ZarrDatasetIOConfiguration.validate_compressors_and_options_length_match()
    • ZarrDatasetIOConfiguration.validate_filters_and_options_length_match()
    • ZarrDatasetIOConfiguration.warn_on_shuffle_in_filters()
    • ZarrDatasetIOConfiguration.compressors
    • ZarrDatasetIOConfiguration.compressor_options
    • ZarrDatasetIOConfiguration.filters
    • ZarrDatasetIOConfiguration.filter_options
  • get_default_backend_configuration()
  • get_default_dataset_io_configurations()
  • get_existing_backend_configuration()
  • get_existing_dataset_io_configurations()
  • configure_backend()
  • add_device_from_metadata()
  • add_subject_to_nwbfile()
  • configure_and_write_nwbfile()
  • get_default_nwbfile_metadata()
  • get_module()
  • make_nwbfile_from_metadata()
  • make_or_load_nwbfile()
  • repack_nwbfile()
• AWS Tools