Merge pull request #16 from catalystneuro/optogenetics

OptogeneticInterface

src/lerner_lab_to_nwb/seiler_2024/__init__.py

@@ -1,3 +1,4 @@
 from .seiler_2024behaviorinterface import Seiler2024BehaviorInterface
 from .seiler_2024fiberphotometryinterface import Seiler2024FiberPhotometryInterface
+from .seiler_2024optogeneticinterface import Seiler2024OptogeneticInterface
 from .seiler_2024nwbconverter import Seiler2024NWBConverter

src/lerner_lab_to_nwb/seiler_2024/seiler_2024_convert_session.py

@@ -18,7 +18,8 @@ def session_to_nwb(
     session_conditions: dict,
     start_variable: str,
     experiment_type: Literal["FP", "Opto"],
-    experimental_group: Literal["DPR", "PR", "PS", "RR20"],
+    experimental_group: Literal["DPR", "PR", "PS", "RR20", "DMS-Inhibitory", "DMS-Excitatory", "DLS-Excitatory"],
+    optogenetic_treatment: Optional[Literal["ChR2", "EYFP", "ChR2Scrambled", "NpHR", "NpHRScrambled"]] = None,
     fiber_photometry_folder_path: Optional[Union[str, Path]] = None,
     stub_test: bool = False,
     verbose: bool = True,
@@ -44,8 +45,10 @@ def session_to_nwb(
         The name of the variable that starts the session (ex. 'Start Date').
     experiment_type : Literal["FP", "Opto"]
         The type of experiment.
-    experimental_group : Literal["DPR", "PR", "PS", "RR20"]
+    experimental_group : Literal["DPR", "PR", "PS", "RR20", "DMS-Inhibitory", "DMS-Excitatory", "DLS-Excitatory"]
         The experimental group.
+    optogenetic_treatment : Optional[Literal["ChR2", "EYFP", "ChR2Scrambled", "NpHR", "NpHRScrambled"]], optional
+        The optogenetic treatment, by default None for FP sessions.
     stub_test : bool, optional
         Whether to run a stub test, by default False
     verbose : bool, optional
@@ -58,9 +61,6 @@ def session_to_nwb(
         output_dir_path = output_dir_path / "nwb_stub"
     output_dir_path.mkdir(parents=True, exist_ok=True)
 
-    nwbfile_path = (
-        output_dir_path / f"{experiment_type}_{experimental_group}_{subject_id}_{start_datetime.isoformat()}.nwb"
-    )
     source_data = {}
     conversion_options = {}
 
@@ -90,6 +90,22 @@ def session_to_nwb(
         )
         conversion_options.update(dict(FiberPhotometry={}))
 
+    # Add Optogenetics
+    if experiment_type == "Opto":
+        source_data.update(
+            dict(
+                Optogenetic={
+                    "file_path": str(behavior_file_path),
+                    "session_conditions": session_conditions,
+                    "start_variable": start_variable,
+                    "experimental_group": experimental_group,
+                    "optogenetic_treatment": optogenetic_treatment,
+                    "verbose": verbose,
+                }
+            )
+        )
+        conversion_options.update(dict(Optogenetic={}))
+
     converter = Seiler2024NWBConverter(source_data=source_data, verbose=verbose)
     metadata = converter.get_metadata()
 
@@ -98,6 +114,19 @@ def session_to_nwb(
     editable_metadata = load_dict_from_file(editable_metadata_path)
     metadata = dict_deep_update(metadata, editable_metadata)
 
+    start_datetime = metadata["NWBFile"]["session_start_time"]
+    if experiment_type == "FP":
+        nwbfile_path = (
+            output_dir_path / f"{experiment_type}_{experimental_group}_{subject_id}_{start_datetime.isoformat()}.nwb"
+        )
+    elif experiment_type == "Opto":
+        nwbfile_path = (
+            output_dir_path
+            / f"{experiment_type}_{experimental_group}_{optogenetic_treatment}_{subject_id}_{start_datetime.isoformat()}.nwb"
+        )
+    else:
+        raise ValueError(f"Invalid experiment type: {experiment_type}")
+
     # Run conversion
     converter.run_conversion(metadata=metadata, nwbfile_path=nwbfile_path, conversion_options=conversion_options)
 
@@ -349,18 +378,237 @@ def session_to_nwb(
     #     stub_test=stub_test,
     # )
 
-    # Behavior session from csv file
-    experiment_type = "FP"
-    experimental_group = "DPR"
-    subject_id = "87.239"
-    start_datetime = datetime(2019, 3, 19, 0, 0, 0)
+    # # Behavior session from csv file
+    # experiment_type = "FP"
+    # experimental_group = "DPR"
+    # subject_id = "87.239"
+    # start_datetime = datetime(2019, 3, 19, 0, 0, 0)
+    # session_conditions = {}
+    # start_variable = ""
+    # behavior_file_path = (
+    #     data_dir_path
+    #     / f"{experiment_type} Experiments"
+    #     / "Behavior"
+    #     / f"{experimental_group}"
+    #     / f"{subject_id}"
+    #     / f"{subject_id}_{start_datetime.strftime('%m-%d-%y')}.csv"
+    # )
+    # session_to_nwb(
+    #     data_dir_path=data_dir_path,
+    #     output_dir_path=output_dir_path,
+    #     behavior_file_path=behavior_file_path,
+    #     subject_id=subject_id,
+    #     session_conditions=session_conditions,
+    #     start_variable=start_variable,
+    #     start_datetime=start_datetime,
+    #     experiment_type=experiment_type,
+    #     experimental_group=experimental_group,
+    #     stub_test=stub_test,
+    # )
+
+    # Example DMS-Inhibitory Opto session
+    experiment_type = "Opto"
+    experimental_group = "DMS-Inhibitory"
+    optogenetic_treatment = "NpHR"
+    subject_id = "112.415"
+    start_datetime = datetime(2020, 10, 21, 13, 8, 39)
+    session_conditions = {
+        "Start Date": start_datetime.strftime("%m/%d/%y"),
+        "Start Time": start_datetime.strftime("%H:%M:%S"),
+    }
+    start_variable = "Start Date"
+    behavior_file_path = (
+        data_dir_path
+        / f"{experiment_type} Experiments"
+        / f"{experimental_group.replace('-', ' ')}"
+        / f"Group 1"
+        / f"Halo"
+        / f"{subject_id}"
+    )
+    session_to_nwb(
+        data_dir_path=data_dir_path,
+        output_dir_path=output_dir_path,
+        behavior_file_path=behavior_file_path,
+        subject_id=subject_id,
+        session_conditions=session_conditions,
+        start_variable=start_variable,
+        start_datetime=start_datetime,
+        experiment_type=experiment_type,
+        experimental_group=experimental_group,
+        optogenetic_treatment=optogenetic_treatment,
+        stub_test=stub_test,
+    )
+
+    # Example DMS-Excitatory Opto session
+    experiment_type = "Opto"
+    experimental_group = "DMS-Excitatory"
+    optogenetic_treatment = "ChR2"
+    subject_id = "119.416"
+    start_datetime = datetime(2020, 10, 20, 13, 0, 57)
+    session_conditions = {
+        "Start Date": start_datetime.strftime("%m/%d/%y"),
+        "Start Time": start_datetime.strftime("%H:%M:%S"),
+    }
+    start_variable = "Start Date"
+    behavior_file_path = (
+        data_dir_path
+        / f"{experiment_type} Experiments"
+        / f"{experimental_group.replace('-', ' ')}"
+        / f"{optogenetic_treatment}"
+        / f"{subject_id}"
+    )
+    session_to_nwb(
+        data_dir_path=data_dir_path,
+        output_dir_path=output_dir_path,
+        behavior_file_path=behavior_file_path,
+        subject_id=subject_id,
+        session_conditions=session_conditions,
+        start_variable=start_variable,
+        start_datetime=start_datetime,
+        experiment_type=experiment_type,
+        experimental_group=experimental_group,
+        optogenetic_treatment=optogenetic_treatment,
+        stub_test=stub_test,
+    )
+
+    # Example DLS-Excitatory Opto session
+    experiment_type = "Opto"
+    experimental_group = "DLS-Excitatory"
+    optogenetic_treatment = "ChR2"
+    subject_id = "079.402"
+    start_datetime = datetime(2020, 6, 26, 13, 19, 27)
+    session_conditions = {
+        "Start Date": start_datetime.strftime("%m/%d/%y"),
+        "Start Time": start_datetime.strftime("%H:%M:%S"),
+    }
+    start_variable = "Start Date"
+    behavior_file_path = (
+        data_dir_path
+        / f"{experiment_type} Experiments"
+        / f"{experimental_group.replace('-', ' ')}"
+        / f"{optogenetic_treatment}"
+        / f"{subject_id}"
+    )
+    session_to_nwb(
+        data_dir_path=data_dir_path,
+        output_dir_path=output_dir_path,
+        behavior_file_path=behavior_file_path,
+        subject_id=subject_id,
+        session_conditions=session_conditions,
+        start_variable=start_variable,
+        start_datetime=start_datetime,
+        experiment_type=experiment_type,
+        experimental_group=experimental_group,
+        optogenetic_treatment=optogenetic_treatment,
+        stub_test=stub_test,
+    )
+
+    # Opto session with both left and right rewards
+    experiment_type = "Opto"
+    experimental_group = "DMS-Excitatory"
+    optogenetic_treatment = "ChR2"
+    subject_id = "281.402"
+    start_datetime = datetime(2020, 9, 23, 12, 36, 30)
+    session_conditions = {
+        "Start Date": start_datetime.strftime("%m/%d/%y"),
+        "Start Time": start_datetime.strftime("%H:%M:%S"),
+    }
+    start_variable = "Start Date"
+    behavior_file_path = (
+        data_dir_path
+        / f"{experiment_type} Experiments"
+        / f"{experimental_group.replace('-', ' ')}"
+        / f"{optogenetic_treatment}"
+        / "2020-09-23_12h36m_Subject 281.402"
+    )
+    session_to_nwb(
+        data_dir_path=data_dir_path,
+        output_dir_path=output_dir_path,
+        behavior_file_path=behavior_file_path,
+        subject_id=subject_id,
+        session_conditions=session_conditions,
+        start_variable=start_variable,
+        start_datetime=start_datetime,
+        experiment_type=experiment_type,
+        experimental_group=experimental_group,
+        optogenetic_treatment=optogenetic_treatment,
+        stub_test=stub_test,
+    )
+
+    # Opto session from csv file
+    experiment_type = "Opto"
+    experimental_group = "DLS-Excitatory"
+    optogenetic_treatment = "ChR2"
+    subject_id = "290.407"
+    start_datetime = datetime(2020, 9, 23, 0, 0, 0)
+    session_conditions = {}
+    start_variable = ""
+    behavior_file_path = (
+        data_dir_path
+        / f"{experiment_type} Experiments"
+        / f"{experimental_group.replace('-', ' ')}"
+        / f"{optogenetic_treatment}"
+        / f"{subject_id}"
+        / f"{subject_id}_{start_datetime.strftime('%m-%d-%y')}.csv"
+    )
+    session_to_nwb(
+        data_dir_path=data_dir_path,
+        output_dir_path=output_dir_path,
+        behavior_file_path=behavior_file_path,
+        subject_id=subject_id,
+        session_conditions=session_conditions,
+        start_variable=start_variable,
+        start_datetime=start_datetime,
+        experiment_type=experiment_type,
+        experimental_group=experimental_group,
+        optogenetic_treatment=optogenetic_treatment,
+        stub_test=stub_test,
+    )
+
+    # Opto session from csv file with scrambled optogenetic stimulation
+    experiment_type = "Opto"
+    experimental_group = "DLS-Excitatory"
+    optogenetic_treatment = "ChR2Scrambled"
+    subject_id = "276.405"
+    start_datetime = datetime(2020, 10, 1, 0, 0, 0)
+    session_conditions = {}
+    start_variable = ""
+    behavior_file_path = (
+        data_dir_path
+        / f"{experiment_type} Experiments"
+        / f"{experimental_group.replace('-', ' ')}"
+        / "Scrambled"
+        / f"{subject_id.replace('.', '_')}"
+        / f"{subject_id}_{start_datetime.strftime('%m-%d-%y')}.csv"
+    )
+    session_to_nwb(
+        data_dir_path=data_dir_path,
+        output_dir_path=output_dir_path,
+        behavior_file_path=behavior_file_path,
+        subject_id=subject_id,
+        session_conditions=session_conditions,
+        start_variable=start_variable,
+        start_datetime=start_datetime,
+        experiment_type=experiment_type,
+        experimental_group=experimental_group,
+        optogenetic_treatment=optogenetic_treatment,
+        stub_test=stub_test,
+    )
+
+    # Could not convert DLS-Excitatory/299.405/09/11/20 00:00:00
+    # Opto session with mixed dtype
+    experiment_type = "Opto"
+    experimental_group = "DLS-Excitatory"
+    optogenetic_treatment = "ChR2"
+    subject_id = "299.405"
+    start_datetime = datetime(2020, 9, 11, 0, 0, 0)
     session_conditions = {}
     start_variable = ""
     behavior_file_path = (
         data_dir_path
         / f"{experiment_type} Experiments"
-        / "Behavior"
-        / f"{experimental_group}"
+        / f"{experimental_group.replace('-', ' ')}"
+        / f"{optogenetic_treatment}"
         / f"{subject_id}"
         / f"{subject_id}_{start_datetime.strftime('%m-%d-%y')}.csv"
     )
@@ -374,5 +622,6 @@ def session_to_nwb(
         start_datetime=start_datetime,
         experiment_type=experiment_type,
         experimental_group=experimental_group,
+        optogenetic_treatment=optogenetic_treatment,
         stub_test=stub_test,
     )

src/lerner_lab_to_nwb/seiler_2024/seiler_2024_metadata.yaml

@@ -167,6 +167,20 @@ Behavior:
       D: right_reward_times
       E: duration_of_port_entry
       G: port_entry_times
+    RI 60 LEFT_STIM:
+      A: left_nose_poke_times
+      B: left_reward_times
+      C: right_nose_poke_times
+      D: right_reward_times
+      E: duration_of_port_entry
+      G: port_entry_times
+    RI 30 LEFT_STIM:
+      A: left_nose_poke_times
+      B: left_reward_times
+      C: right_nose_poke_times
+      D: right_reward_times
+      E: duration_of_port_entry
+      G: port_entry_times
     RI30 Left Scrambled:
       A: left_nose_poke_times
       B: left_reward_times
@@ -223,3 +237,38 @@ Behavior:
       E: duration_of_port_entry
       G: port_entry_times
       H: footshock_times
+
+Optogenetics:
+  experimental_group_to_metadata:
+    DMS-Excitatory:
+      injection_location: medial SNc (AP -3.1, ML 0.8, DV -4.7)
+      stimulation_location: DMS (AP 0.8, ML 1.5, DV -2.8)
+      excitation_lambda: 460.0 # nm
+      ogen_site_description: Mice for DMS excitatory optogenetics experiments received 1 ml of AAV5-EF1a-DIO-hChR2(H134R)-EYFP (3.3e13 GC/mL, Addgene, lot v17652) or the control fluorophore-only virus AAV5-EF1a-DIO-EYFP (3.5e12 virus molecules/mL, UNC Vector Core, lot AV4310K) in medial (AP -3.1, ML 0.8, DV -4.7) and a single fiber optic implant (Prizmatix; 250mm core, 0.66 NA) over ipsilateral DMS (AP 0.8, ML 1.5, DV -2.8). Hemispheres were counterbalanced between mice.
+      ogen_series_description: During operant training (beginning with FR1), each rewarded nosepoke was paired with a train of blue light (460nm, 1 s, 20 Hz, 15 mW) generated by an LED light source and pulse generator (Prizmatix). A subset of mice ("ChR2 Scrambled") received the same train of light but paired with random nosepokes on a separate RI60 schedule.
+      duration: 1.0 # seconds
+      frequency: 20.0 # Hz
+      pulse_width: 0.01 # TODO: ask Lerner lab for pulse width
+      power: 0.015 # W
+
+    DLS-Excitatory:
+      injection_location: lateral SNc  (AP -3.1, ML 1.3, DV -4.2)
+      stimulation_location: DLS (AP -0.1, ML 2.8, DV -3.5)
+      excitation_lambda: 460.0 # nm
+      ogen_site_description: Mice for DLS excitatory optogenetics experiments received 1 ml of AAV5-EF1a-DIO-hChR2(H134R)-EYFP (3.3e13 GC/mL, Addgene, lot v17652) or the control fluorophore-only virus AAV5-EF1a-DIO-EYFP (3.5e12 virus molecules/mL, UNC Vector Core, lot AV4310K) in lateral SNc (AP -3.1, ML 1.3, DV -4.2) and a single fiber optic implant (Prizmatix; 250mm core, 0.66 NA) over ipsilateral DLS (AP -0.1, ML 2.8, DV -3.5). Hemispheres were counterbalanced between mice.
+      ogen_series_description: During operant training (beginning with FR1), each rewarded nosepoke was paired with a train of blue light (460nm, 1 s, 20 Hz, 15 mW) generated by an LED light source and pulse generator (Prizmatix). A subset of mice ("ChR2 Scrambled") received the same train of light but paired with random nosepokes on a separate RI60 schedule.
+      duration: 1.0 # seconds
+      frequency: 20.0 # Hz
+      pulse_width: 0.01 # TODO: ask Lerner lab for pulse width
+      power: 0.015 # W
+
+    DMS-Inhibitory:
+      injection_location: bilateral medial SNc (AP -3.1, ML ± 0.8, DV -4.7)
+      stimulation_location: bilateral DMS (AP 0.8, ML ± 1.5, DV -2.8)
+      excitation_lambda: 625.0 # nm
+      ogen_site_description: Mice for DMS inhibitory optogenetics experiments received 1 ml per side of AAV5-EF1a-DIO-eNpHR3.0-EYFP (1.1e13 GC/mL, Addgene, lot v32533) or the control fluorophore-only virus AAV5-EF1a-DIO-EYFP (3.5e12 virus molecules/mL, UNC Vector Core, lot AV4310K) in bilateral medial SNc (AP -3.1, ML 0.8, DV -4.7) and bilateral fiber optic implants (Prizmatix; 500mm core, 0.66 NA) in DMS (AP 0.8, ML ± 1.5, DV -2.8).
+      ogen_series_description:  There were two groups of inhibitory optogenetics animals. Group 1 received inhibitory stimulation during operant training beginning with FR1, Since a subset of animals in this group were unable to learn the operant task, we also ran another group (Group 2) that received inhibitory stimulation during operant training beginning with RI30. These groups are combined for analysis of behaviors occurring after RI training has begun. For both groups, each rewarded nosepoke was paired with a continuous pulse of orange/red light (625nm, 1 s, 15 mW) generated by an LED light source and pulse generator (Prizmatix). A subset of mice ("NpHR Scrambled") received the same continuous pulse of light but paired with random nosepokes on a separate RI60 schedule.
+      duration: 1.0 # seconds
+      frequency: 1.0 # Hz
+      pulse_width: 1.0 # seconds
+      power: 0.015 # W