Add ThorTiffImagingInterface

docs/api/interfaces.ophys.rst

@@ -29,6 +29,10 @@ ScanImage Imaging
 -----------------
 .. automodule:: neuroconv.datainterfaces.ophys.scanimage.scanimageimaginginterfaces
 
+ThorLabs Imaging
+----------------
+.. automodule:: neuroconv.datainterfaces.ophys.thor.thorimaginginterface
+
 Tiff Imaging
 ------------
 .. automodule:: neuroconv.datainterfaces.ophys.tiff.tiffdatainterface

docs/conversion_examples_gallery/imaging/thor.rst

@@ -0,0 +1,29 @@
+ThorLabs data conversion
+------------------------
+
+Install NeuroConv with the additional dependencies necessary for reading ThorLabs imaging data.
+
+.. code-block:: bash
+
+    pip install neuroconv[thor]
+
+Convert single plane single file imaging data
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Convert ScanImage imaging data to NWB using
+:py:class:`~neuroconv.datainterfaces.ophys.thor.thorimaginginterface`.
+
+.. code-block:: python
+
+    >>> from datetime import datetime
+    >>> from dateutil import tz
+    >>> from pathlib import Path
+    >>> from neuroconv.datainterfaces import ThorTiffImagingInterface
+    >>>
+    >>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "ThorLabs" / "data"
+    >>> interface = ThorTiffImagingInterface(folder_path=folder_path)
+    >>>
+    >>> metadata = interface.get_metadata()
+    >>>
+    >>> # Choose a path for saving the nwb file and run the conversion
+    >>> interface.run_conversion(nwbfile_path=f"{path_to_save_nwbfile}", metadata=metadata)

src/neuroconv/datainterfaces/__init__.py

@@ -87,6 +87,7 @@
 )
 from .ophys.sima.simadatainterface import SimaSegmentationInterface
 from .ophys.suite2p.suite2pdatainterface import Suite2pSegmentationInterface
+from .ophys.thor.thorimaginginterface import ThorTiffImagingInterface
 from .ophys.tiff.tiffdatainterface import TiffImagingInterface
 
 # Text
@@ -138,6 +139,7 @@
     ExtractSegmentationInterface,
     SimaSegmentationInterface,
     SbxImagingInterface,
+    ThorTiffImagingInterface,
     TiffImagingInterface,
     Hdf5ImagingInterface,
     ScanImageImagingInterface,

src/neuroconv/datainterfaces/ophys/thor/requirements.txt

@@ -0,0 +1 @@
+roiextractors[thor]

src/neuroconv/datainterfaces/ophys/thor/thorimaginginterface.py

@@ -0,0 +1,40 @@
+from roiextractors.extractors.thorextractors.thorimagingextractor import (
+    ThorTiffImagingExtractor,
+)
+
+from neuroconv.datainterfaces.ophys.baseimagingextractorinterface import (
+    BaseImagingExtractorInterface,
+)
+from neuroconv.utils import DeepDict, FilePathType
+
+
+class ThorTiffImagingInterface(BaseImagingExtractorInterface):
+    """Interface for multi-page TIFF files from the ThorLabs acquisition system."""
+
+    display_name = "ThorLabs TIFF Imaging"
+    Extractor = ThorTiffImagingExtractor
+
+    @classmethod
+    def get_source_schema(cls) -> dict:
+        source_schema = super().get_source_schema()
+        source_schema["properties"]["folder_path"]["description"] = (
+            "Directory that contains the TIFF files and " "Experiment.xml file. "
+        )
+        return source_schema
+
+    def __init__(self, folder_path: FilePathType, verbose: bool = False):
+        """
+        Initialize reading of TIFF file.
+
+        Parameters
+        ----------
+        folder_path : FilePathType
+            Directory that contains the TIFF files and Experiment.xml file.
+        verbose : bool, default: False
+        """
+        super().__init__(folder_path=folder_path, verbose=verbose)
+
+    def get_metadata(self, photon_series_type="TwoPhotonSeries") -> DeepDict:
+        metadata = super().get_metadata(photon_series_type=photon_series_type)
+        metadata["NWBFile"]["session_start_time"] = self.extractor.start_time
+        return metadata