Intan Data Conversion#

This guide covers the conversion of Intan data, including both amplifier data (primary neural recordings) and analog data (auxiliary inputs, ADC inputs, DC amplifiers) from RHD2000 and RHS2000 systems.

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

pip install "neuroconv[intan]"

Intan Amplifier Data Conversion#

Convert Intan amplifier data to NWB using IntanRecordingInterface. This interface handles the primary neural recordings from the RHD2000 or RHS2000 amplifier channels.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import IntanRecordingInterface
>>>
>>> file_path = f"{ECEPHY_DATA_PATH}/intan/intan_rhd_test_1.rhd" # This can also be .rhs
>>> interface = IntanRecordingInterface(file_path=file_path, verbose=False)
>>>
>>> # 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)
>>>
>>> nwbfile_path = f"{path_to_save_nwbfile}"  # This should be something like: "./saved_file.nwb"
>>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True)

Intan Analog Data Conversion#

Convert non-amplifier analog data from Intan systems to NWB using IntanAnalogInterface. This includes signals from auxiliary inputs, ADC inputs, and DC amplifiers.

This interface supports analog streams including:

USB board ADC input channel: ADC input channels
RHD2000 auxiliary input channel: Auxiliary input channels (e.g., accelerometer data)
DC Amplifier channel: DC amplifier channels (RHS system only)
USB board ADC output channel: ADC output channels

USB board ADC input channels#

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import IntanAnalogInterface
>>>
>>> # For this interface we need to pass the location of the .rhd or .rhs file
>>> file_path = f"{ECEPHY_DATA_PATH}/intan/intan_rhd_test_1.rhd"
>>>
>>> # Convert ADC input channels
>>> interface = IntanAnalogInterface(
...     file_path=file_path,
...     stream_name="USB board ADC input channel",
...     verbose=False
... )
>>>
>>> # Extract what metadata we can from the source files
>>> metadata = interface.get_metadata()
>>> # session_start_time is required but not available on intan
>>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, 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, overwrite=True)

RHD2000 auxiliary input#

You can also convert auxiliary input channels (e.g., accelerometer data):

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import IntanAnalogInterface
>>>
>>> # For this interface we need to pass the location of the .rhd or .rhs file
>>> file_path_aux = f"{ECEPHY_DATA_PATH}/intan/intan_fpc_test_231117_052630/info.rhd"
>>>
>>> # Convert auxiliary input channels (e.g., accelerometer data)
>>> interface_aux = IntanAnalogInterface(
...     file_path=file_path_aux,
...     stream_name="RHD2000 auxiliary input channel",
...     verbose=False
... )
>>>
>>> # Extract what metadata we can from the source files
>>> metadata_aux = interface_aux.get_metadata()
>>> # session_start_time is required but not available on intan
>>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=ZoneInfo("US/Pacific"))
>>> metadata_aux["NWBFile"].update(session_start_time=session_start_time)
>>>
>>> # Choose a path for saving the nwb file and run the conversion
>>> nwbfile_path_aux = output_folder / "intan_auxiliary_conversion.nwb"
>>> interface_aux.run_conversion(nwbfile_path=nwbfile_path_aux, metadata=metadata_aux, overwrite=True)

DC Amplifier channels (RHS systems)#

For RHS systems, you can also convert DC amplifier channels:

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import IntanAnalogInterface
>>>
>>> # For this interface we need to pass the location of the .rhs file
>>> file_path_dc = f"{ECEPHY_DATA_PATH}/intan/test_fcs_dc_250327_154333/info.rhs"
>>>
>>> # Convert DC amplifier channels (RHS system)
>>> interface_dc = IntanAnalogInterface(
...     file_path=file_path_dc,
...     stream_name="DC Amplifier channel",
...     verbose=False
... )
>>>
>>> # Extract what metadata we can from the source files
>>> metadata_dc = interface_dc.get_metadata()
>>> # session_start_time is required but not available on intan
>>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, tzinfo=ZoneInfo("US/Pacific"))
>>> metadata_dc["NWBFile"].update(session_start_time=session_start_time)
>>>
>>> # Choose a path for saving the nwb file and run the conversion
>>> nwbfile_path_dc = output_folder / "intan_dc_amplifier_conversion.nwb"
>>> interface_dc.run_conversion(nwbfile_path=nwbfile_path_dc, metadata=metadata_dc, overwrite=True)

USB board ADC output channels (RHS systems)#

For RHS systems, you can also convert ADC output channels:

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import IntanAnalogInterface
>>>
>>> # For this interface we need to pass the location of the .rhs file
>>> file_path_output = f"{ECEPHY_DATA_PATH}/intan/rhs_stim_data_single_file_format/intanTestFile.rhs"
>>>
>>> # Convert ADC output channels (RHS system)
>>> interface_output = IntanAnalogInterface(
...     file_path=file_path_output,
...     stream_name="USB board ADC output channel",
...     verbose=False
... )
>>>
>>> # Extract what metadata we can from the source files
>>> metadata_output = interface_output.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_output["NWBFile"].update(session_start_time=session_start_time)
>>>
>>> # Choose a path for saving the nwb file and run the conversion
>>> nwbfile_path_output = output_folder / "intan_adc_output_conversion.nwb"
>>> interface_output.run_conversion(nwbfile_path=nwbfile_path_output, metadata=metadata_output, overwrite=True)