suite2p

Install NeuroConv with the additional dependencies necessary for reading suite2p data.

pip install "neuroconv[suite2p]"

Convert suite2p segmentation data to NWB using Suite2pSegmentationInterface.

Suite2p segmentation output is saved for each plane in a separate folder (e.g. “plane0”, “plane1”). To specify which plane to convert, use the plane_name argument (to see what planes are available use the Suite2pSegmentationInterface.get_available_planes(folder_path) method). For multichannel recordings, use the channel_name argument to specify the channel name (to see what channels are available use the Suite2pSegmentationInterface.get_channel_names(folder_path) method). When not specified, the first plane and channel are used.

The optional plane_segmentation_name argument specifies the name of the PlaneSegmentation to be created. When multiple planes and/or channels are present, the name should be unique for each plane and channel combination (e.g. “PlaneSegmentationChan1Plane0”).

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import Suite2pSegmentationInterface
>>>
>>> folder_path= OPHYS_DATA_PATH / "segmentation_datasets" / "suite2p"
>>> interface = Suite2pSegmentationInterface(folder_path=folder_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)

Multi-plane example

This example shows how to convert multiple planes from the same dataset.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv import ConverterPipe
>>> from neuroconv.datainterfaces import Suite2pSegmentationInterface
>>>
>>> folder_path= OPHYS_DATA_PATH / "segmentation_datasets" / "suite2p"
>>> interface_first_plane = Suite2pSegmentationInterface(folder_path=folder_path, plane_name="plane0", verbose=False)
>>> interface_second_plane = Suite2pSegmentationInterface(folder_path=folder_path, plane_name="plane1", verbose=False)
>>>
>>> converter = ConverterPipe(data_interfaces=[interface_first_plane, interface_second_plane], verbose=False)
>>> metadata = converter.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"{output_folder}/file2.nwb"
>>> converter.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)