CaImAn

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

pip install "neuroconv[caiman]"

Convert CaImAn segmentation data to NWB using CaimanSegmentationInterface.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import CaimanSegmentationInterface
>>>
>>> file_path = OPHYS_DATA_PATH / "segmentation_datasets" / "caiman" / "caiman_analysis.hdf5"
>>> interface = CaimanSegmentationInterface(file_path=file_path, 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)