OpenEphys data conversion

OpenEphys supports two data formats: the Binary (.dat) format and the Open Ephys (.continuous) format. The OpenEphysRecordingInterface supports both formats and auto-detects which one to use based on the files present in the folder.

Install NeuroConv with the additional dependencies necessary for reading OpenEphys data.

pip install "neuroconv[openephys]"

Convert OpenEphys data to NWB using OpenEphysRecordingInterface.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>>
>>> from neuroconv.datainterfaces import OpenEphysRecordingInterface
>>>
>>> folder_path = f"{ECEPHY_DATA_PATH}/openephysbinary/v0.4.4.1_with_video_tracking"
>>> # Change the folder_path to the appropriate location in your system
>>> interface = OpenEphysRecordingInterface(folder_path=folder_path)
>>> # Extract what metadata we can from the source files
>>> metadata = interface.get_metadata()
>>> # session_start_time is required for conversion. If it cannot be inferred
>>> # automatically from the source files you must supply one.
>>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=ZoneInfo("US/Pacific"))
>>> metadata["NWBFile"].update(session_start_time=session_start_time)
>>> # Add subject information (required for DANDI upload)
>>> metadata["Subject"] = dict(subject_id="subject1", species="Mus musculus", sex="M", age="P30D")
>>>
>>> # Choose a path for saving the nwb file and run the conversion
>>> nwbfile_path = f"{path_to_save_nwbfile}"  # This should be something like: "./saved_file.nwb"
>>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

OpenEphysBinaryConverter

For multi-stream OpenEphys binary recordings (e.g. Neuropixels with AP, LFP, and analog streams), use OpenEphysBinaryConverter to convert all streams at once. When AP and LFP streams come from the same probe, the converter automatically shares electrode table rows between them.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from neuroconv.converters import OpenEphysBinaryConverter
>>>
>>> folder_path = f"{ECEPHY_DATA_PATH}/openephysbinary/v0.6.x_neuropixels_with_sync"
>>> # Change the folder_path to the appropriate location in your system
>>> converter = OpenEphysBinaryConverter(folder_path=folder_path)
>>> # 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 = metadata["NWBFile"]["session_start_time"].replace(tzinfo=ZoneInfo("US/Pacific"))
>>> metadata["NWBFile"].update(session_start_time=session_start_time)
>>> # Add subject information (required for DANDI upload)
>>> metadata["Subject"] = dict(subject_id="subject1", species="Mus musculus", sex="M", age="P30D")
>>>
>>> # Choose a path for saving the nwb file and run the conversion
>>> nwbfile_path = output_folder / "my_openephys_binary_converter_session.nwb"
>>> converter.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

Note

The OpenEphysBinaryConverter only supports the Binary (.dat) format. There is currently no converter for the Open Ephys (.continuous) format. If you need multi-stream conversion support for Open Ephys (.continuous) format data, please open an issue.