ScanImage Legacy (v3.8 and older)

Install the package with the additional dependencies necessary for reading ScanImage TIFF files (v3.8 and older) using the legacy reader:

pip install neuroconv[scanimage_legacy]

Convert ScanImage TIFF files to NWB using ScanImageTiffInterface.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import ScanImageLegacyImagingInterface
>>>
>>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "Tif" / "sample_scanimage.tiff"
>>>
>>> # The fallback_sampling_frequency is only needed if the sampling frequency
>>> # cannot be extracted from the file metadata
>>> interface = ScanImageLegacyImagingInterface(
...     file_path=file_path,
...     fallback_sampling_frequency=30.0,  # Optional: only if not in metadata
... )
>>>
>>> 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, overwrite=True)

The ScanImageLegacyImagingInterface interface uses the scanimage-tiff-reader package for reading legacy ScanImage TIFF files that may not be compatible with the standard TIFF readers.

Note

This interface is specifically for legacy ScanImage files. For newer ScanImage files, use the regular ScanImageTiffInterface with the scanimage extra instead.