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)
>>> # Add subject information (required for DANDI upload)
>>> metadata["Subject"] = dict(subject_id="subject1", species="Mus musculus", sex="M", age="P30D")
>>>
>>> # 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)

NeuroConv aims to automatically add all the metadata annotations that are present in the source format. It is often the case that crucial information is not available there, such as the anatomical location, the meaning of the values, or a semantically meaningful description of the data. Follow the ophys how-to for a modality-relevant guide to adding this extra metadata, which makes the data more useful for future users and for the community as a whole. Its section on templates starts from scratch, and the reference template lists every element the metadata accepts.

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.