Merge pull request #9 from catalystneuro/opto

Opto

src/schneider_lab_to_nwb/schneider_2024/__init__.py

@@ -1,3 +1,4 @@
 from .schneider_2024_behaviorinterface import Schneider2024BehaviorInterface
+from .schneider_2024_optogeneticinterface import Schneider2024OptogeneticInterface
 from .schneider_2024_intrinsic_signal_imaging_interface import Schneider2024IntrinsicSignalOpticalImagingInterface
 from .schneider_2024_nwbconverter import Schneider2024NWBConverter

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_convert_session.py

@@ -60,6 +60,10 @@ def session_to_nwb(
         source_data.update({metadata_key_name: dict(file_paths=[video_file_path], metadata_key_name=metadata_key_name)})
         conversion_options.update({metadata_key_name: dict()})
 
+    # Add Optogenetic
+    source_data.update(dict(Optogenetic=dict(file_path=behavior_file_path)))
+    conversion_options.update(dict(Optogenetic=dict()))
+
     # Add Intrinsic Signal Optical Imaging
     source_data.update(dict(ISOI=dict(folder_path=intrinsic_signal_optical_imaging_folder_path)))
     conversion_options.update(dict(ISOI=dict()))
@@ -118,7 +122,7 @@ def main():
     sorting_folder_path = (
         data_dir_path / "Schneider sample Data" / "Processed Ephys" / "m69_2023-10-31_17-24-15_Day1_A1"
     )
-    behavior_file_path = data_dir_path / "NWB_Share" / "Sample behavior data" / "m74_ephysSample.mat"
+    behavior_file_path = data_dir_path / "NWB_Share" / "Sample behavior data" / "m74_optoSample.mat"
     video_folder_path = data_dir_path / "Schneider sample Data" / "Video" / "m69_231031"
     intrinsic_signal_optical_imaging_folder_path = data_dir_path / "NWB_Share" / "Sample Intrinsic imaging data"
     session_to_nwb(

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_metadata.yaml

@@ -88,6 +88,22 @@ Behavior:
 Sorting:
   units_description: Neural spikes will be sorted offline using Kilosort 2.5 and Phy2 software and manually curated to ensure precise spike time acquisition.
 
+Optogenetics:
+  Device:
+    name: optogenetic_stimulation_laser
+    description: Real time optogenetic stimulation of brain regions of interest will be accomplished via TTL control of an all solidstate 473nm blue laser (MBL-III-473/1~100mW, Opto Engine LLC). Bifurcated fiber cables (ThorLabs, Ø200 µm Core Multimode Fiber) will be used for light delivery.
+    manufacturer: Opto Engine LLC
+  OptogeneticStimulusSite:
+    name: optogenetic_stimulus_site
+    description: To identify cortical neurons that project from the auditory cortex to motor regions (Aim 2), stereotaxic injections of AAV-ChR2 will be made into the primary auditory cortex (-2.8 AP, 4.2 ML relative to bregma; guided by intrinsic optical imaging) during head-fixation and animals will be trained while expression occurs (~2 weeks). In addition, fiber optics will be implanted to target cell bodies in the secondary motor cortex (1.0-1.5 AP, 0.5-0.7 ML).
+    excitation_lambda: 473.0 # nm
+    injection_location: Primary Auditory Cortex  (-2.8 AP, 4.2 ML relative to bregma; guided by intrinsic optical imaging)
+    stimulation_location: Secondary Motor Cortex (1.0-1.5 AP, 0.5-0.7 ML)
+  OptogeneticSeries:
+    name: optogenetic_series
+    description: In optogenetic perturbation trials (~33% of trials), during each lever press, continuous wave stimulation of 473nm light (15-20mW) will be delivered bilaterally over primary auditory cortex A1 (or secondary motor cortex, M2, as necessary using similar protocol - see Aim 2) to activate the terminals of ChR2 expressing neurons.
+    power: 0.020 # 15-20 mW
+
 IntrinsicSignalOpticalImaging:
   Module:
     name: intrinsic_signal_optical_imaging

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_notes.md

@@ -4,13 +4,18 @@
 
 ## Video
 
+## Optogenetics
+- is_opto_trial in the trials table is `np.logical_not(np.isnan(onset_times))` rather than reading from the .mat file
+    to ensure consistency with the onset/offset times.
+
 ## Intrinsic Signal Optical Imaging
 - Just including raw blood vessel image and processed overlay + pixel locations bc including the isoi roi response series would really require an extension for context, but seems like it has limited reuse potential.
 - Used the Audette paper for description of overlay image.
 - Need pixel locs for ephys
 - Need device info for 2p microscope and red light laser
 - Why is the overlaid image flipped left/right compared to the original?
 
+
 ## Data Requests
 - Mice sexes
 - Remaining data for Grant's project

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_nwbconverter.py

@@ -9,6 +9,7 @@
 
 from schneider_lab_to_nwb.schneider_2024 import (
     Schneider2024BehaviorInterface,
+    Schneider2024OptogeneticInterface,
     Schneider2024IntrinsicSignalOpticalImagingInterface,
 )
 
@@ -22,5 +23,6 @@ class Schneider2024NWBConverter(NWBConverter):
         Behavior=Schneider2024BehaviorInterface,
         VideoCamera1=VideoInterface,
         VideoCamera2=VideoInterface,
+        Optogenetic=Schneider2024OptogeneticInterface,
         ISOI=Schneider2024IntrinsicSignalOpticalImagingInterface,
     )

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_optogeneticinterface.py

@@ -0,0 +1,78 @@
+"""Primary class for converting optogenetic stimulation."""
+from pynwb.file import NWBFile
+from pydantic import FilePath
+import numpy as np
+from pymatreader import read_mat
+from pynwb.device import Device
+from pynwb.ogen import OptogeneticSeries, OptogeneticStimulusSite
+
+from neuroconv.basedatainterface import BaseDataInterface
+from neuroconv.utils import DeepDict
+
+
+class Schneider2024OptogeneticInterface(BaseDataInterface):
+    """Optogenetic interface for schneider_2024 conversion"""
+
+    keywords = ["optogenetics"]
+
+    def __init__(self, file_path: FilePath):
+        super().__init__(file_path=file_path)
+
+    def get_metadata(self) -> DeepDict:
+        metadata = super().get_metadata()
+
+        return metadata
+
+    def get_metadata_schema(self) -> dict:
+        metadata_schema = super().get_metadata_schema()
+        return metadata_schema
+
+    def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
+        # Read Data
+        file_path = self.source_data["file_path"]
+        file = read_mat(file_path)
+        onset_times = file["events"]["push"]["opto_time"]
+        is_opto_trial = np.logical_not(np.isnan(onset_times))
+        onset_times = onset_times[is_opto_trial]
+        offset_times = file["events"]["push"]["opto_time_end"]
+        offset_times = offset_times[is_opto_trial]
+        assert np.all(
+            np.logical_not(np.isnan(offset_times))
+        ), "Some of the offset times are nan when onset times are not nan."
+        power = metadata["Optogenetics"]["OptogeneticSeries"]["power"]
+
+        timestamps, data = [], []
+        for onset_time, offset_time in zip(onset_times, offset_times):
+            timestamps.append(onset_time)
+            data.append(power)
+            timestamps.append(offset_time)
+            data.append(0)
+        timestamps, data = np.array(timestamps, dtype=np.float64), np.array(data, dtype=np.float64)
+
+        # Add Data to NWBFile
+        # Add Device
+        device = Device(**metadata["Optogenetics"]["Device"])
+        nwbfile.add_device(device)
+
+        # Add OptogeneticStimulusSite
+        site_metadata = metadata["Optogenetics"]["OptogeneticStimulusSite"]
+        location = f"Injection location: {site_metadata['injection_location']} \n Stimulation location: {site_metadata['stimulation_location']}"
+        ogen_site = OptogeneticStimulusSite(
+            name=site_metadata["name"],
+            device=device,
+            description=site_metadata["description"],
+            excitation_lambda=site_metadata["excitation_lambda"],
+            location=location,
+        )
+        nwbfile.add_ogen_site(ogen_site)
+
+        # Add OptogeneticSeries
+        series_metadata = metadata["Optogenetics"]["OptogeneticSeries"]
+        optogenetic_series = OptogeneticSeries(
+            name=series_metadata["name"],
+            site=ogen_site,
+            description=series_metadata["description"],
+            data=data,
+            timestamps=timestamps,
+        )
+        nwbfile.add_stimulus(optogenetic_series)