Tiff & Suite2p

A common workflow in optical physiology is to record images with a microscope (imaging) and then use a segmentation algorithm to produce regions of interest and fluorescence traces. The following is an example of who to implement this workflow in neuroconv for Tiff imaging files segmented using suite2p. This conversion uses the classes TiffImagingInterface and Suite2pSegmentationInterface.

>>> from datetime import datetime
>>> from zoneinfo import ZoneInfo
>>> from pathlib import Path
>>> from neuroconv import ConverterPipe
>>> from neuroconv.datainterfaces import TiffImagingInterface, Suite2pSegmentationInterface
>>>
>>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "Tif" / "demoMovie.tif"
>>> interface_tiff = TiffImagingInterface(file_path=file_path, sampling_frequency=15.0, verbose=False)
>>>
>>> folder_path= OPHYS_DATA_PATH / "segmentation_datasets" / "suite2p"
>>> interface_suit2p = Suite2pSegmentationInterface(folder_path=folder_path, verbose=False)
>>>
>>> # Now that we have defined the two interfaces we pass them to the ConverterPipe which will coordinate the
>>> # concurrent conversion of the data
>>> converter = ConverterPipe(data_interfaces=[interface_tiff, interface_suit2p], verbose=False)
>>>
>>> # Extract what metadata we can from the source files
>>> metadata = converter.get_metadata()
>>> # For data provenance we add the time zone information to the conversion
>>> session_start_time = datetime(2020, 1, 1, 12, 30, 0, 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}"
>>> converter.run_conversion(nwbfile_path=nwbfile_path,  metadata=metadata)