Merge pull request #22 from catalystneuro/add_subject_metadata

Add subject metadata and generate session description for each session

src/cai_lab_to_nwb/zaki_2024/utils/__init__.py

@@ -11,3 +11,4 @@
     get_freezing_output_file_path,
 )
 from .define_conversion_parameters import update_conversion_parameters_yaml
+from .generate_session_description import generate_session_description

src/cai_lab_to_nwb/zaki_2024/utils/conversion_parameters.yaml

@@ -7,6 +7,11 @@ Ca_EEG2-1:
     imaging_folder_path: D:\Ca_EEG_Experiment\Ca_EEG2-1\Ca_EEG2-1_Sessions\Ca_EEG2-1_FC\10_11_24
     minian_folder_path: D:\Ca_EEG_Calcium\Ca_EEG2-1\Ca_EEG2-1_FC\minian
     output_dir_path: D:\cai_lab_conversion_nwb
+    session_description: 'Fear Conditioning session: after a baseline period of 2
+      min, mouse received three 2s foot shocks of 1.5, with an intershock interval
+      of 1 min. Then, 30 s after the final shock, the mice were removed and returned
+      to the vivarium. Context: overhead external light, external fan at medium level,
+      box fan on, even grid floor, acetic acid 1pct scent'
     session_id: Ca_EEG2-1_FC
     shock_stimulus:
       shock_amplitude: 1.5

src/cai_lab_to_nwb/zaki_2024/utils/define_conversion_parameters.py

@@ -1,7 +1,8 @@
 import re
 import yaml
 
-from source_data_path_resolver import *
+from .source_data_path_resolver import *
+from .generate_session_description import generate_session_description
 
 
 def update_conversion_parameters_yaml(
@@ -55,7 +56,7 @@ def update_conversion_parameters_yaml(
             sleep_classification_file_path = None
             video_file_path = get_video_file_path(subject_id, session_id, data_dir_path)
             freezing_output_file_path = get_freezing_output_file_path(subject_id, session_id, data_dir_path)
-            if session_type == "FC":
+            if session_type == "FC" or session_type == "Recall1":
                 shock_amplitude = subjects_df["Amplitude"][subjects_df["Mouse"] == subject_id].to_numpy()[0]
                 shock_amplitude = float(re.findall(r"[-+]?\d*\.\d+|\d+", shock_amplitude)[0])
                 shock_stimulus = dict(
@@ -65,13 +66,18 @@ def update_conversion_parameters_yaml(
                 shock_stimulus = None
         imaging_folder_path = get_imaging_folder_path(subject_id, session_id, data_dir_path, time_str, date_str)
         minian_folder_path = get_miniscope_folder_path(subject_id, session_id, data_dir_path)
+
+        session_description = generate_session_description(
+            experiment_design_file_path=experiment_design_file_path, subject_id=subject_id, session_type=session_type
+        )
         session_to_nwb_kwargs_per_session = {
             session_id: {
                 "output_dir_path": str(output_dir_path),
                 "subject_id": subject_id,
                 "session_id": session_id,
                 "date_str": date_str,
                 "time_str": time_str,
+                "session_description": session_description,
                 "experiment_dir_path": str(experiment_dir_path),
                 "imaging_folder_path": str(imaging_folder_path) if imaging_folder_path else None,
                 "minian_folder_path": str(minian_folder_path) if minian_folder_path else None,
@@ -103,7 +109,7 @@ def update_conversion_parameters_yaml(
 
 if __name__ == "__main__":
     update_conversion_parameters_yaml(
-        subject_id="Ca_EEG2-1",
+        subject_id="Ca_EEG3-4",
         data_dir_path=Path("D:/"),
         output_dir_path=Path("D:/cai_lab_conversion_nwb/"),
         experiment_design_file_path=Path("D:/Ca_EEG_Design.xlsx"),

src/cai_lab_to_nwb/zaki_2024/utils/generate_session_description.py

@@ -0,0 +1,40 @@
+from pathlib import Path
+from typing import Union
+import pandas as pd
+import re
+
+
+def generate_session_description(experiment_design_file_path: Union[Path, str], subject_id: str, session_type: str):
+    subjects_df = pd.read_excel(experiment_design_file_path)
+    subject_df = subjects_df[subjects_df["Mouse"] == subject_id]
+    shock_amplitude = subject_df["Amplitude"].to_numpy()[0]
+    shock_amplitude = float(re.findall(r"[-+]?\d*\.\d+|\d+", shock_amplitude)[0])
+
+    Contexts = {
+        "A": "overhead external light, external fan off, box fan on, smooth floor, white curve insert, simple green 5pct scent",
+        "B": "overhead external light, external fan off, box fan on, bath mat floor, A frame insert, ethanol 70pct scent",
+        "S": "overhead external light, external fan at medium level, box fan on, even grid floor, acetic acid 1pct scent",
+    }
+
+    session_descriptions = {
+        "NeutralExposure": f"Neutral Exposure session: mouse was exposed to a neutral context for 10 min to explore. Context: {Contexts["A"]}",
+        "FC": f"Fear Conditioning session: after a baseline period of 2 min, mouse received three 2s foot shocks of {shock_amplitude}, with an intershock interval of 1 min. Then, 30 s after the final shock, the mice were removed and returned to the vivarium. Context: {Contexts["S"]}",
+        "Recall1": f"First Recall session: mouse was placed in shock context for 5 min. Context: {Contexts['S']}",
+        "Recall2": f"Second Recall session: mouse was placed in {subject_df["Test_2"].to_numpy()[0]} context for 5 min. Context: {Contexts[subject_df["Test_2_ctx"].to_numpy()[0]]}",
+        "Recall3": f"Third Recall session: mouse was placed in {subject_df["Test_3"].to_numpy()[0]} context for 5 min. Context: {Contexts[subject_df["Test_3_ctx"].to_numpy()[0]]}",
+        "Offline": f"After Neutral Exposure and Fear Conditioning sessions, mice were taken out of the testing chambers and immediately placed in their homecage (scope was not removed).The homecage was placed in a dark grey storage bin with a webcam on top of the bin, taped to a wooden plank, looking down into the homecage. Mouse behavior and calcium were recorded for an hour.",
+    }
+    if "Offline" in session_type:
+        session_type = "Offline"
+
+    return session_descriptions[session_type]
+
+
+if __name__ == "__main__":
+    experiment_design_file_path = Path("D:/Ca_EEG_Design.xlsx")
+    subject_id = "Ca_EEG3-4"
+    session_type = "NeutralExposure"
+    session_description = generate_session_description(
+        experiment_design_file_path=experiment_design_file_path, subject_id=subject_id, session_type=session_type
+    )
+    print(session_description)

src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py

@@ -19,8 +19,9 @@ def session_to_nwb(
     session_id: str,
     date_str: str,
     time_str: str,
+    session_description: str,
     stub_test: bool = False,
-    verbose: bool = True,
+    verbose: bool = False,
     experiment_dir_path: Union[str, Path] = None,
     imaging_folder_path: Union[str, Path] = None,
     minian_folder_path: Union[str, Path] = None,
@@ -237,6 +238,7 @@ def session_to_nwb(
     metadata = dict_deep_update(metadata, editable_metadata)
 
     metadata["Subject"]["subject_id"] = subject_id
+    metadata["NWBFile"]["session_description"] = session_description
 
     # Run conversion
     converter.run_conversion(

src/cai_lab_to_nwb/zaki_2024/zaki_2024_metadata.yaml

@@ -10,23 +10,22 @@ NWBFile:
     - aversive
   related_publications:
     - https://doi.org/10.1038/s41586-024-08168-4
-  session_description:
-    In memory-linking behavioural experiments, mice were exposed to the neutral context for 10 min to explore. 
-    During aversive encoding, after a baseline period of 2 min, mice received three 2 s foot shocks of either amplitude 
-    0.25 mA (low-shock) or 1.5 mA (high-shock), with an intershock interval of 1 min. 
-    Then, 30 s after the final shock, the mice were removed and returned to the vivarium. 
-    On the next 3 days, the mice were tested in the previously experienced aversive and neutral contexts, 
-    as well as a completely novel context that they had not been exposed to previously, for 5 min each. 
-    The features of the neutral and novel contexts were counter-balanced and were made up of different olfactory, 
-    auditory, lighting and tactile cues. 
-    The aversive context was always the same with distinct cues from the neutral and novel contexts. 
-    In the low- versus high-shock experiments mice were tested in the aversive context first, 
-    followed by testing in the neutral and novel context counter-balanced; 
-    half of the mice received neutral recall and then novel-context exposure the next day, 
-    and the other half received novel-context exposure and then neutral recall.
   experiment_description:
     Simultaneous calcium imaging with Miniscopes and EEG/EMG experiment during retrospective memory-linking behavioral paradigm, 
-    to test whether ensemble co-reactivation is sleep-state specific
+    to test whether ensemble co-reactivation is sleep-state specific.
+    Mice were exposed to the neutral context for 10 min to explore.
+    During aversive encoding, after a baseline period of 2 min, mice received three 2 s foot shocks of either amplitude
+    0.25 mA (low-shock) or 1.5 mA (high-shock), with an intershock interval of 1 min.
+    Then, 30 s after the final shock, the mice were removed and returned to the vivarium.
+    On the next 3 days, the mice were tested in the previously experienced aversive and neutral contexts,
+    as well as a completely novel context that they had not been exposed to previously, for 5 min each.
+    The features of the neutral and novel contexts were counter-balanced and were made up of different olfactory,
+    auditory, lighting and tactile cues.
+    The aversive context was always the same with distinct cues from the neutral and novel contexts.
+    In the low- versus high-shock experiments mice were tested in the aversive context first,
+    followed by testing in the neutral and novel context counter-balanced;
+    half of the mice received neutral recall and then novel-context exposure the next day,
+    and the other half received novel-context exposure and then neutral recall.
   institution: Icahn School of Medicine at Mount Sinai
   lab: Cai
   experimenter:
@@ -35,14 +34,38 @@ NWBFile:
     Mice were anaesthetized with 1 to 2% isoflurane for surgical procedures and placed into a stereotaxic frame (David Kopf Instruments). 
     Eye ointment was applied to prevent desiccation, and the mice were kept on a heated pad to prevent hypothermia. 
     Surgery was performed using aseptic technique. After surgery, carprofen (5mg per kg) was administered every day for the following 3 days, 
-    and ampicillin (20mg per kg) was administered every day for the next 7days. 
-    For calcium imaging experiments, dexamethasone (0.2mg per kg) was also administered for the following 7days.
+    and ampicillin (20mg per kg) was administered every day for the next 7days.
+    For calcium imaging experiments with EEG/EMG implants, mice underwent three serial procedures spaced around 2 weeks apart. 
+    During the first surgery, mice had 300 nl of AAV1-Syn-GCaMP6f injected into dorsal CA1 (AP, −2 mm; ML, +1.5 mm; DV, −1.2 mm), 
+    the incision was sutured after the surgery.    
+    Then, 2 weeks later during a second surgery, mice had their overlying cortex aspirated and a GRIN lens was implanted above the injection site. 
+    This involved aspirating the cortex with a 27-gauge blunt syringe needle attached to a vacuum pump, constantly irrigating with cortex buffer. 
+    When the striations of the corpus callosum were visible, a 30-gauge needle replaced the 27-gauge needle for finer-tuned aspiration. 
+    Once most of corpus callosum was removed, bleeding was controlled using surgical foam (Surgifoam), 
+    and a 1 mm diameter x 4 mm length GRIN lens (GRINTECH) was slowly lowered into the craniotomy. 
+    The lens was fixed with cyanoacrylate, and dental acrylic was applied to cement the implant in place and cover the exposed skull. 
+    The top of the exposed lens was covered with Kwik-Sil (World Precision Instruments) and then dental cement.
+    During this same surgery, a wireless telemetry probe (HD-X02, Data Science International) was implanted with EEG and EMG wires. 
+    Two EMG wires were placed into the left trapezius muscle. 
+    One EEG wire was implanted between the skull and dura mater above the dorsal hippocampus on the contralateral hemisphere to the GRIN lens 
+    (left hemisphere; AP, −2 mm; ML, −1.5 mm), and a reference EEG wire was implanted between the skull and the dura on the right hemisphere overlying the prefrontal cortex (AP, +1.75 mm; ML, −0.5 mm). 
+    Cyanoacrylate and dental cement fixed the GRIN lens, anchor screw, and EEG wires in place. 
+    The telemetry probes were implanted during this second surgery to minimize the time mice needed to live with the implant.
+    During the third procedure, the mice were returned to implant the baseplate. 
+    The Miniscope with an attached baseplate was lowered near the implanted lens, with the field of view monitored in real-time on a computer. 
+    The Miniscope was rotated until a well-exposed field of view was observed, at which point the baseplate was fixed to the implant with cyanoacrylate and dental cement.
   virus:
     AAV1-Syn-GCaMP6f was injected into dorsal CA1 of the hippocampus on the right hemisphere (AP, −2 mm; ML, +1.5 mm; DV, −1.2 mm)
 Subject:
   species: Mus musculus
-  age: P12W/P15W  # in ISO 8601, such as "P1W2D"
+  description: Adult C57BL/6J wild-type mice from Jackson Laboratories were used. 
+    Mice ordered from Jackson arrived group-housed in cages of 4 mice/cage and were singly housed for the experiment. 
+    Mice were ordered to arrive at 8-9 weeks of age and underwent behavioral testing about 4-6 weeks after the arrival date. 
+    All experimental procedures were approved by the Icahn School of Medicine at Mount Sinai’s IACUC.
+  age: P12W/P18W
   sex: M
+  strain: C57BL/6J
+  genotype: wild-type
 Ophys:
   OnePhotonSeries:
     - name: OnePhotonSeries