add inscopix imaging extractor and test

docs/api/interfaces.ophys.rst

@@ -13,6 +13,10 @@ HDF5 Imaging
 ------------
 .. automodule:: neuroconv.datainterfaces.ophys.hdf5.hdf5datainterface
 
+Inscopix Imaging
+----------------
+.. automodule:: neuroconv.datainterfaces.ophys.inscopix.inscopiximaginginterface
+
 MicroManager Tiff Imaging
 -------------------------
 .. automodule:: neuroconv.datainterfaces.ophys.micromanagertiff.micromanagertiffdatainterface

docs/conversion_examples_gallery/conversion_example_gallery.rst

@@ -66,6 +66,7 @@ Imaging
 
     Bruker <imaging/brukertiff>
     HDF5 <imaging/hdf5imaging>
+    Inscopix <imaging/inscopix>
     Micro-Manager <imaging/micromanagertiff>
     Miniscope <imaging/miniscope>
     Scanbox <imaging/scanbox>

docs/conversion_examples_gallery/imaging/inscopix.rst

@@ -0,0 +1,29 @@
+Inscopix data conversion
+------------------------
+
+Install NeuroConv with the additional dependencies necessary for reading Inscopix imaging data form .isxd files.
+
+.. code-block:: bash
+
+    pip install neuroconv[inscopix]
+
+Convert Inscopix .isxd imaging data to NWB using :py:class:`~neuroconv.datainterfaces.ophys.inscopix.inscopiximaginginterface.InscopixImagingInterface`.
+
+.. code-block:: python
+
+    >>> from datetime import datetime
+    >>> from dateutil import tz
+    >>> from pathlib import Path
+    >>> from neuroconv.datainterfaces import InscopixImagingInterface
+    >>>
+    >>> file_path = OPHYS_DATA_PATH / "imaging_datasets" / "inscopix" / "movie_longer_than_3_min.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"]
+    >>> 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)

src/neuroconv/datainterfaces/__init__.py

@@ -76,6 +76,7 @@
 from .ophys.cnmfe.cnmfedatainterface import CnmfeSegmentationInterface
 from .ophys.extract.extractdatainterface import ExtractSegmentationInterface
 from .ophys.hdf5.hdf5datainterface import Hdf5ImagingInterface
+from .ophys.inscopix.inscopiximaginginterface import InscopixImagingInterface
 from .ophys.micromanagertiff.micromanagertiffdatainterface import (
     MicroManagerTiffImagingInterface,
 )
@@ -146,6 +147,7 @@
     BrukerTiffSinglePlaneImagingInterface,
     MicroManagerTiffImagingInterface,
     MiniscopeImagingInterface,
+    InscopixImagingInterface,
     # Behavior
     VideoInterface,
     AudioInterface,

src/neuroconv/datainterfaces/ophys/inscopix/inscopiximaginginterface.py

@@ -0,0 +1,47 @@
+from datetime import datetime
+from imaplib import Literal
+
+from ..baseimagingextractorinterface import BaseImagingExtractorInterface
+from ....utils import DeepDict, FilePathType
+
+
+class InscopixImagingInterface(BaseImagingExtractorInterface):
+    """Interface for Inscopix imaging data."""
+
+    display_name = "Inscopix Imaging"
+    associated_suffixes = (".isxd",)
+    info = "Interface for Inscopix imaging data."
+
+    def __init__(self, file_path: FilePathType, verbose: bool = True):
+        """
+
+        Parameters
+        ----------
+        file_path : FilePathType
+            Path to .isxd file.
+        verbose : bool, default: True
+        """
+        super().__init__(file_path=file_path, verbose=verbose)
+
+    def get_metadata(
+        self, photon_series_type: Literal["OnePhotonSeries", "TwoPhotonSeries"] = "TwoPhotonSeries"
+    ) -> DeepDict:
+        metadata = super().get_metadata(photon_series_type=photon_series_type)
+
+        extra_props = self.imaging_extractor.movie.footer["extraProperties"]
+
+        if extra_props["animal"]["id"]:
+            metadata["Subject"]["subject_id"] = extra_props["animal"]["id"]
+        if extra_props["animal"]["species"]:
+            metadata["Subject"]["species"] = extra_props["animal"]["species"]
+        if extra_props["animal"]["sex"]:
+            metadata["Subject"]["sex"] = extra_props["animal"]["sex"].upper()
+        if extra_props["animal"]["dob"]:
+            metadata["Subject"]["date_of_birth"] = extra_props["animal"]["dob"]
+        if extra_props["animal"]["weight"]:
+            metadata["Subject"]["weight"] = str(extra_props["animal"]["weight"])
+
+        if extra_props["date"]:
+            metadata["NWBFile"]["session_start_time"] = datetime.strptime(extra_props["date"], "%Y-%m-%dT%H:%M:%S.%fZ")
+
+        return metadata

src/neuroconv/datainterfaces/ophys/requirements.txt

@@ -1 +1 @@
-roiextractors>=0.5.7
+roiextractors>=0.6.0

tests/test_on_data/test_imaging_interfaces.py

@@ -14,6 +14,7 @@
     BrukerTiffMultiPlaneImagingInterface,
     BrukerTiffSinglePlaneImagingInterface,
     Hdf5ImagingInterface,
+    InscopixImagingInterface,
     MicroManagerTiffImagingInterface,
     MiniscopeImagingInterface,
     SbxImagingInterface,
@@ -805,3 +806,11 @@ def check_incorrect_folder_structure_raises(self):
             exc_type=AssertionError, exc_msg="The main folder should contain at least one subfolder named 'Miniscope'."
         ):
             self.data_interface_cls(folder_path=folder_path)
+
+
+class TestInscopixImagingInterface(ImagingExtractorInterfaceTestMixin, TestCase):
+    data_interface_cls = InscopixImagingInterface
+    interface_kwargs = dict(
+        file_path=str(OPHYS_DATA_PATH / "imaging_datasets" / "inscopix" / "movie_longer_than_3_min.isxd")
+    )
+    save_directory = OUTPUT_PATH