Inscopix imaging data conversion

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

pip install "neuroconv[inscopix]"

Convert Inscopix imaging data to NWB using InscopixImagingInterface.

>>> import sys, platform
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv.datainterfaces import InscopixImagingInterface
>>>
>>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "inscopix" / "movie_128x128x100_part1.isxd"
>>> interface = InscopixImagingInterface(file_path=file_path, 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)
>>> # Add subject information (required for DANDI upload)
>>> metadata["Subject"] = dict(subject_id="subject1", species="Mus musculus", sex="M", age="P30D")
>>>
>>> # Run the conversion
>>> nwbfile_path = f"{path_to_save_nwbfile}"
>>> interface.run_conversion(nwbfile_path=nwbfile_path, metadata=metadata)

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.