added opto

src/schneider_lab_to_nwb/schneider_2024/__init__.py

@@ -1,2 +1,3 @@
 from .schneider_2024_behaviorinterface import Schneider2024BehaviorInterface
+from .schneider_2024_optogeneticinterface import Schneider2024OptogeneticInterface
 from .schneider_2024_nwbconverter import Schneider2024NWBConverter

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_convert_session.py

@@ -59,6 +59,10 @@ 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()))
+
     converter = Schneider2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
@@ -113,7 +117,7 @@ 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"
     session_to_nwb(
         recording_folder_path=recording_folder_path,

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_metadata.yaml

@@ -87,3 +87,18 @@ 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 AC to motor regions (Aim 2), stereotaxic injections of AAV-ChR2 will be made into AC (-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 striatum (+ 0.9 AP, 1.8 ML, -2.3 DV).
+    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: Striatum (+ 0.9 AP, 1.8 ML, -2.3 DV)
+  OptogeneticSeries:
+    name: optogenetic_series
+    description: On experiment day before recording, 100ms pulses of 473nm light will be delivered over striatum (or secondary motor cortex, M2, as necessary using similar protocol - see Aim 2) to activate the terminals of ChR2 expressing neurons (Figure 4A), generating antidromic spikes in the direction towards AC whereby we can then identify motor-regionprojecting AC cells via offline analysis of action potential latency to the light stimulus (see preliminary data Aim 2).

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_notes.md

@@ -4,6 +4,13 @@
 
 ## Video
 
+## Optogenetics
+- How to distinguish between 473nm stim in striatum w/ AAV-ChR2 and 532nm stim in A1 w/ AAV-FLEx-Arch+AAV-Retro-Cre?
+- Opto stim frequency?
+- Per trial power? 100mW? 300mW?
+- Pulse width for 532nm stim (also 100ms)?
+- There is one trial at the end of the behavioral session that is 1 for opto_trial but nan for stim onset and offset times. What to do?
+
 ## Data Requests
 - Mice sexes
 - Remaining data for Grant's project

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_nwbconverter.py

@@ -7,7 +7,7 @@
 )
 from neuroconv.basedatainterface import BaseDataInterface
 
-from schneider_lab_to_nwb.schneider_2024 import Schneider2024BehaviorInterface
+from schneider_lab_to_nwb.schneider_2024 import Schneider2024BehaviorInterface, Schneider2024OptogeneticInterface
 
 
 class Schneider2024NWBConverter(NWBConverter):
@@ -19,4 +19,5 @@ class Schneider2024NWBConverter(NWBConverter):
         Behavior=Schneider2024BehaviorInterface,
         VideoCamera1=VideoInterface,
         VideoCamera2=VideoInterface,
+        Optogenetic=Schneider2024OptogeneticInterface,
     )