Electrophysiology and Behavior

This example showcases a conversion that combines two modalities of data electrophysiology and behavior in the form of pose estimation. For this specific example were are combining a OpenEphys recording with KiloSort sorting results and PoseEstimation from sleap using the BlackrockRecordingInterface, KiloSortSortingInterface, and SLEAPInterface. classes.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv import ConverterPipe
>>> from neuroconv.datainterfaces import BlackrockRecordingInterface, KiloSortSortingInterface, SLEAPInterface
>>>
>>>
>>> file_path = f"{ECEPHY_DATA_PATH}/blackrock/FileSpec2.3001.ns5"
>>> # Change the file_path to the location in your system
>>> interface_blackrock = BlackrockRecordingInterface(file_path=file_path, verbose=False)
>>>
>>> folder_path = f"{ECEPHY_DATA_PATH}/phy/phy_example_0"
>>> # Change the folder_path to the location of the data in your system
>>> interface_kilosort = KiloSortSortingInterface(folder_path=folder_path, verbose=False)
>>>
>>> # Change the file_path so it points to the slp file in your system
>>> file_path = BEHAVIOR_DATA_PATH / "sleap" / "predictions_1.2.7_provenance_and_tracking.slp"
>>> interface_sleap = SLEAPInterface(file_path=file_path, verbose=False)
>>>
>>> # Now that we have defined the two interfaces we pass them to the ConverterPipe which will coordinate the
>>> # concurrent conversion of the data
>>> converter = ConverterPipe(data_interfaces=[interface_blackrock, interface_kilosort, interface_sleap], verbose=False)
>>>
>>> # Extract what metadata we can from the source files
>>> metadata = converter.get_metadata()
>>> # For data provenance we add the time zone information to the conversion
>>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=ZoneInfo("US/Pacific")).isoformat()
>>> metadata["NWBFile"].update(session_start_time=session_start_time)
>>>
>>> # Choose a path for saving the nwb file and run the conversion
>>> nwbfile_path = f"{path_to_save_nwbfile}"
>>> converter.run_conversion(nwbfile_path=nwbfile_path,  metadata=metadata)