EXTRACT

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

pip install "neuroconv[extract]"

Convert EXTRACT segmentation data to NWB using ExtractSegmentationInterface.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import ExtractSegmentationInterface
>>>
>>> file_path = OPHYS_DATA_PATH / "segmentation_datasets" / "extract"/ "2014_04_01_p203_m19_check01_extractAnalysis.mat"
>>> sampling_frequency = 20.0 # The sampling frequency in units of Hz
>>> interface = ExtractSegmentationInterface(file_path=file_path, sampling_frequency=sampling_frequency, verbose=False)
>>>
>>> metadata = interface.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"))
>>> 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)