ScanImage data conversion

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

pip install "neuroconv[scanimage]"

Convert ScanImage imaging data

The ScanImageImagingInterface handles both single and multi-file data, as well as multi-channel data. For multi-channel data, you need to specify the channel name, and you can use plane_index if you want to only write a specific plane.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import ScanImageImagingInterface
>>>
>>>
>>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "ScanImage" / "volumetric_single_channel_single_file_no_flyback" / "vol_no_flyback_00001_00001.tif"
>>>
>>> # Specify channel_name for multi-channel data
>>> # Specify plane_index for selecting a specific plane in multi-plane data or leave undefined  to write volumetric data
>>> interface = ScanImageImagingInterface(
...     file_path=file_path,
...     channel_name="Channel 1",  # Required for multi-channel data
...     plane_index=None,  # Optional: specify to only write a specific plane
... )
>>> metadata = interface.get_metadata()
>>> # For data provenance we add the time zone information to the conversion
>>> session_start_time = metadata["NWBFile"]["session_start_time"].replace(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)

Note

For older ScanImage files (v3.8 and earlier), use the ScanImageLegacyImagingInterface interface instead.