ABF data conversion

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

pip install "neuroconv[abf]"

Convert ABF intracellular electrophysiology data to NWB using AbfInterface.

>>> from neuroconv.datainterfaces import AbfInterface
>>>
>>> # Metadata info
>>> icephys_metadata = {
...     "cell_id": "20220818001",
...     "slice_id": "20220818001",
...     "targeted_layer": "L2-3(medial)",
...     "inferred_layer": "",
...     "recording_sessions": [
...         {
...             "abf_file_name": "File_axon_5.abf",
...             "stimulus_type": "long_square",
...             "icephys_experiment_type": "voltage_clamp"
...         }
...     ]
... }
>>>
>>> # Instantiate data interface
>>> interface = AbfInterface(
...     file_paths=[f"{ECEPHY_DATA_PATH}/axon/File_axon_5.abf"],
...     icephys_metadata=icephys_metadata
... )
>>>
>>> # Get metadata from source data and modify any values you want
>>> metadata = interface.get_metadata()
>>> metadata['NWBFile'].update(
...     identifier="ID1234",
...     session_description="Intracellular electrophysiology experiment.",
...     lab="my lab name",                       # <-- optional
...     institution="My University",             # <-- optional
...     experimenter=["John Doe", "Jane Doe"],   # <-- optional
... )
>>> metadata["Subject"] = dict(
...     subject_id="subject_ID123",
...     species="Mus musculus",
...     sex="M",
...     date_of_birth="2022-03-15T00:00:00"
... )
>>>
>>> # Run conversion
>>> interface.run_conversion(nwbfile_path=output_folder / "single_abf_conversion.nwb", metadata=metadata)

If you have multiple ABF files for the same experiment, one file per recording stimulus type, you can organize a multi-file conversion as such:

>>> from neuroconv.datainterfaces import AbfInterface
>>>
>>> # Metadata info
>>> icephys_metadata = {
...     "cell_id": "20220818001",
...     "slice_id": "20220818001",
...     "targeted_layer": "L2-3(medial)",
...     "inferred_layer": "",
...     "recording_sessions": [
...         {
...             "abf_file_name": "File_axon_5.abf",
...             "stimulus_type": "long_square",
...             "icephys_experiment_type": "voltage_clamp"
...         },
...         {
...             "abf_file_name": "File_axon_6.abf",
...             "stimulus_type": "short_square",
...             "icephys_experiment_type": "voltage_clamp"
...         }
...     ]
... }
>>>
>>> # Instantiate data interface
>>> interface = AbfInterface(
...     file_paths=[
...         f"{ECEPHY_DATA_PATH}/axon/File_axon_5.abf",
...         f"{ECEPHY_DATA_PATH}/axon/File_axon_6.abf",
...     ],
...     icephys_metadata=icephys_metadata
... )
>>>
>>> # Get metadata from source data and modify any values you want
>>> metadata = interface.get_metadata()
>>> metadata['NWBFile'].update(
...     identifier="ID1234",
...     session_description="Intracellular electrophysiology experiment.",
...     lab="my lab name",                       # <-- optional
...     institution="My University",             # <-- optional
...     experimenter=["John Doe", "Jane Doe"],   # <-- optional
... )
>>> metadata["Subject"] = dict(
...     subject_id="subject_ID123",
...     species="Mus musculus",
...     sex="M",
...     date_of_birth="2022-03-15T00:00:00"
... )
>>>
>>> # Run conversion
>>> interface.run_conversion(nwbfile_path=output_folder / "multiple_abf_conversion.nwb", metadata=metadata)