Add holographic stimulation for Two Photon Imaging (#23)

* fix plane map for single plane single color

* add holography metadata to converter

* add holography interface

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* add tutorials

* temporary pin ndx-holographic-stimulation

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* add metadata

* update metadata.yaml

* update metadata schema for holographicstimulationdatainterface

* temporary pin to `ndx-holographic-stimulation` commit

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* update tutorial

* Add group name to holographic stimulation plane seg table

* refresh tutorial

* Update src/pinto_lab_to_nwb/into_the_void/into_the_void_requirements.txt

* update tutorial

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/pinto_lab_to_nwb/into_the_void/holographic_stimulation_metadata.yaml

@@ -0,0 +1,25 @@
+Ophys:
+  OptogeneticDevice:
+    SpatialLightModulator:
+      name: spatial_light_modulator
+      description: |
+        NeuraLight 3D SLM Module for Photoactivation Pathway, multi-region, holographic stimulation
+        and activation module using 512 x 512 spatial light modulator with Overdrive technology.
+      manufacturer: NeuraLight
+    LightSource:
+      name: light_source
+      description: |
+        The Coherent Monaco laser used for holographic stimulation with 251 fs pulse width and 2 MHz pulse rate.
+      stimulation_wavelength: 1035.0 # nm
+      power: 700.0 # the peak power of stimulation in Watts
+      filter_description: short pass 1040 nm filter
+      intensity: 0.005 # the intensity of excitation in Watts
+      exposure_time: 0.000000000000251 # the exposure time of the sample in seconds
+      pulse_rate: 2000000.0 # the pulse rate of the laser is in Hz
+  OptogeneticStimulusSite:
+    - name: site
+      description: |
+        The targeted location of the holographic stimulation.
+      excitation_lambda: 1050.0 # nm
+      effector: ChRmine # the peak power of stimulation in Watts
+      location: soma # should be the targeted brain area

src/pinto_lab_to_nwb/into_the_void/interfaces/__init__.py

@@ -0,0 +1 @@
+from .holographicstimulationdatainterface import HolographicStimulationInterface

src/pinto_lab_to_nwb/into_the_void/into_the_void_convert_session.py

@@ -67,6 +67,12 @@ def session_to_nwb(
     editable_metadata = load_dict_from_file(editable_metadata_path)
     metadata = dict_deep_update(metadata, editable_metadata)
 
+    # Update metadata with the holographic stimulation data
+    if "HolographicStimulation" in converter.data_interface_objects:
+        holographic_stimulation_metadata_path = Path(__file__).parent / "holographic_stimulation_metadata.yaml"
+        holographic_metadata = load_dict_from_file(holographic_stimulation_metadata_path)
+        metadata = dict_deep_update(metadata, holographic_metadata)
+
     # Update metadata with subject_id and session_id from folder_path
     # NCCR51_2023_04_07_no_task_dual_color_jrgeco_t_series-001
     file_naming_pattern = r"^(?P<subject_id>[^_]+)_(?:\d{4}_\d{2}_\d{2}_)(?P<session_id>.+)"

src/pinto_lab_to_nwb/into_the_void/into_the_void_requirements.txt

@@ -1 +1,3 @@
-neuroconv[suite2p, brukertiff]
+neuroconv[suite2p, brukertiff] @ git+https://github.com/catalystneuro/neuroconv.git@main
+ndx-holographic-stimulation @ git+https://github.com/catalystneuro/ndx-holographic-stimulation.git@423512fd37bff329b7bab708089d51c8cf91e4f7
+hdmf @ git+https://github.com/hdmf-dev/hdmf.git@dev

src/pinto_lab_to_nwb/into_the_void/into_the_voidnwbconverter.py

@@ -1,11 +1,14 @@
 """Primary NWBConverter class for this dataset."""
+from pathlib import Path
 from typing import Optional
 
 from ndx_pinto_metadata import SubjectExtension
 from neuroconv import NWBConverter
 from neuroconv.datainterfaces import Suite2pSegmentationInterface, BrukerTiffMultiPlaneImagingInterface
 from neuroconv.converters import BrukerTiffSinglePlaneConverter, BrukerTiffMultiPlaneConverter
-from neuroconv.utils import FolderPathType, DeepDict
+
+from pinto_lab_to_nwb.into_the_void.interfaces import HolographicStimulationInterface
+from neuroconv.utils import FolderPathType, DeepDict, dict_deep_update
 from pynwb import NWBFile
 
 
@@ -27,26 +30,25 @@ def get_default_segmentation_to_imaging_name_mapping(
         plane_separation_type="disjoint",
     )
 
+    plane_streams = [
+        plane_name for channel_name in streams["plane_streams"] for plane_name in streams["plane_streams"][channel_name]
+    ]
+
     available_channels = Suite2pSegmentationInterface.get_available_channels(folder_path=segmentation_folder_path)
     available_planes = Suite2pSegmentationInterface.get_available_planes(folder_path=segmentation_folder_path)
 
-    if len(available_planes) == 1 and len(available_channels) == 1:
-        return None
-
     segmentation_channel_plane_names = [
         f"{channel_name.capitalize()}{plane_name.capitalize()}"
         for plane_name in available_planes
         for channel_name in available_channels
     ]
 
-    if len(available_planes) > 1:
-        imaging_channel_plane_names = [
-            plane_name
-            for channel_name in streams["plane_streams"]
-            for plane_name in streams["plane_streams"][channel_name]
-        ]
+    num_channels = len(streams["channel_streams"])
+    num_planes = 1 if not plane_streams else len(plane_streams)
+    if num_channels == 1 and num_planes == 1:
+        imaging_channel_plane_names = [None]
     else:
-        imaging_channel_plane_names = streams["channel_streams"]
+        imaging_channel_plane_names = plane_streams if num_planes == 1 else streams["channel_streams"]
 
     segmentation_to_imaging_name_mapping = dict(zip(segmentation_channel_plane_names, imaging_channel_plane_names))
 
@@ -88,6 +90,13 @@ def __init__(
                 Imaging=BrukerTiffSinglePlaneConverter(folder_path=imaging_folder_path, verbose=verbose),
             )
 
+        if list(Path(imaging_folder_path).glob("*MarkPoints*.xml")):
+            self.data_interface_objects.update(
+                HolographicStimulation=HolographicStimulationInterface(
+                    folder_path=imaging_folder_path, verbose=verbose
+                ),
+            )
+
         if segmentation_folder_path:
             available_planes = Suite2pSegmentationInterface.get_available_planes(folder_path=segmentation_folder_path)
             available_channels = Suite2pSegmentationInterface.get_available_channels(
@@ -120,9 +129,10 @@ def __init__(
                         verbose=verbose,
                     )
                     if self.plane_map:
-                        plane_segmentation_name = "PlaneSegmentation" + self.plane_map.get(
-                            plane_name_suffix, None
-                        ).replace("_", "")
+                        mapped_plane_suffix = self.plane_map.get(plane_name_suffix, None)
+                        plane_segmentation_name = "PlaneSegmentation"
+                        if mapped_plane_suffix is not None:
+                            plane_segmentation_name = "PlaneSegmentation" + mapped_plane_suffix.replace("_", "")
                         segmentation_source_data.update(
                             plane_segmentation_name=plane_segmentation_name,
                         )
@@ -132,9 +142,6 @@ def __init__(
                     )
 
     def get_metadata(self) -> DeepDict:
-        if not self.plane_map:
-            return super().get_metadata()
-
         imaging_metadata = self.data_interface_objects["Imaging"].get_metadata()
         metadata = super().get_metadata()
 
@@ -151,6 +158,10 @@ def get_metadata(self) -> DeepDict:
             # override device link
             metadata["Ophys"]["ImagingPlane"][metadata_ind]["device"] = device_name
 
+        if "HolographicStimulation" in self.data_interface_objects:
+            holographic_metadata = self.data_interface_objects["HolographicStimulation"].get_metadata()
+            metadata = dict_deep_update(metadata, holographic_metadata)
+
         return metadata
 
     def add_to_nwbfile(self, nwbfile: NWBFile, metadata, conversion_options: Optional[dict] = None) -> None: