SpikeGLX data conversion

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

pip install "neuroconv[spikeglx]"

SpikeGLXConverter

We can easily convert all data stored in the native SpikeGLX folder structure to NWB using SpikeGLXConverterPipe.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.converters import SpikeGLXConverterPipe
>>>
>>> folder_path = f"{ECEPHY_DATA_PATH}/spikeglx/Noise4Sam_g0"
>>> converter = SpikeGLXConverterPipe(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)
>>>
>>> # Choose a path for saving the nwb file and run the conversion
>>> nwbfile_path = output_folder / "my_spikeglx_session.nwb"
>>> converter.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

Single-stream

Defining a ‘stream’ as a single band on a single NeuroPixels probe, we can convert either an AP or LF SpikeGLX stream to NWB using SpikeGLXRecordingInterface.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import SpikeGLXRecordingInterface
>>>
>>> # For this interface we need to pass the location of the ``.bin`` file
>>> folder_path = f"{ECEPHY_DATA_PATH}/spikeglx/Noise4Sam_g0/Noise4Sam_g0_imec0"
>>> # Options for the streams are "imec0.ap", "imec0.lf", "imec1.ap", "imec1.lf", etc.
>>> # Depending on the device and the band of interest, choose the appropriate stream
>>> interface = SpikeGLXRecordingInterface(folder_path=folder_path, stream_id="imec0.ap", verbose=False)
>>>
>>> # Extract what metadata we can from the source files
>>> metadata = interface.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)
>>>
>>> # Choose a path for saving the nwb file and run the conversion
>>> nwbfile_path = f"{path_to_save_nwbfile}"
>>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)