ScanImage data conversion

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

pip install "neuroconv[scanimage]"

Convert single plane single file imaging data

Convert ScanImage imaging data to NWB using ScanImageImagingInterface.

>>> 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" / "scanimage_20220923_roi.tif"
>>> interface = ScanImageImagingInterface(file_path=file_path, channel_name="Channel 1", plane_name="0", verbose=False)
>>>
>>> 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)

Convert multi-plane (volumetric) single file imaging data

Convert ScanImage volumetric imaging data to NWB using ScanImageImagingInterface.

>>> 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" / "scanimage_20220923_roi.tif"
>>> interface = ScanImageImagingInterface(file_path=file_path, channel_name="Channel 1", verbose=False)
>>>
>>> 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"{output_folder}/scanimage_multi_plane.nwb"
>>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

Convert single plane multi-file (buffered) imaging data

Convert multi-file ScanImage imaging data to NWB using ScanImageMultiFileImagingInterface.

>>> from zoneinfo import ZoneInfo
>>> from neuroconv.datainterfaces import ScanImageMultiFileImagingInterface
>>>
>>> folder_path = OPHYS_DATA_PATH / "imaging_datasets" / "ScanImage"
>>> file_pattern = "scanimage_20240320_multifile*.tif"
>>> channel_name = "Channel 1"
>>> interface = ScanImageMultiFileImagingInterface(folder_path=folder_path, file_pattern=file_pattern, channel_name=channel_name, verbose=False)
>>>
>>> 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"{output_folder}/scanimage_single_plane_multi_file.nwb"
>>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

Convert multi-plane (volumetric) multi-file (buffered) imaging data

Convert volumetric multi-file ScanImage imaging data to NWB using ScanImageMultiPlaneMultiFileImagingInterface.

>>> from zoneinfo import ZoneInfo
>>> from neuroconv.datainterfaces import ScanImageMultiFileImagingInterface
>>>
>>> folder_path = OPHYS_DATA_PATH / "imaging_datasets" / "ScanImage"
>>> file_pattern = "scanimage_20220923_roi.tif"
>>> channel_name = "Channel 1"
>>> interface = ScanImageMultiFileImagingInterface(folder_path=folder_path, file_pattern=file_pattern, channel_name=channel_name, verbose=False)
>>>
>>> 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"{output_folder}/scanimage_multi_plane_multi_file.nwb"
>>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)