Merge branch 'main' into add_week_long_session

src/cai_lab_to_nwb/zaki_2024/interfaces/__init__.py

@@ -3,3 +3,4 @@
 from .minian_interface import MinianSegmentationInterface, MinianMotionCorrectionInterface
 from .zaki_2024_sleep_classification_interface import Zaki2024SleepClassificationInterface
 from .miniscope_imaging_interface import MiniscopeImagingInterface
+from .zaki_2024_shock_stimuli_interface import Zaki2024ShockStimuliInterface

src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py

@@ -352,6 +352,7 @@ def add_to_nwbfile(
         photon_series_index: int = 0,
         stub_test: bool = False,
         stub_frames: int = 100,
+        always_write_timestamps: bool = True,
     ):
         from ndx_miniscope.utils import add_miniscope_device
 
@@ -379,4 +380,5 @@ def add_to_nwbfile(
             metadata=metadata,
             photon_series_type=photon_series_type,
             photon_series_index=photon_series_index,
+            always_write_timestamps=always_write_timestamps,
         )

src/cai_lab_to_nwb/zaki_2024/interfaces/zaki_2024_shock_stimuli_interface.py

@@ -0,0 +1,50 @@
+"""Primary class for converting experiment-specific behavior."""
+
+from pynwb.file import NWBFile
+
+from neuroconv.basedatainterface import BaseDataInterface
+from neuroconv.utils import DeepDict
+from typing import Optional, List
+from pynwb.epoch import TimeIntervals
+
+
+class Zaki2024ShockStimuliInterface(BaseDataInterface):
+    """Adds annotated events of shock times."""
+
+    keywords = ["behavior", "sleep stages"]
+
+    def __init__(self, verbose: bool = False):
+
+        self.verbose = verbose
+        super().__init__()
+
+    def get_metadata(self) -> DeepDict:
+        # Automatically retrieve as much metadata as possible from the source files available
+        metadata = super().get_metadata()
+
+        return metadata
+
+    def add_to_nwbfile(
+        self,
+        nwbfile: NWBFile,
+        shock_amplitude: float,
+        shock_times: list,
+        shock_duration: float,
+        metadata: Optional[dict] = None,
+    ):
+
+        description = (
+            "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. "
+            "All testing was done in Med Associates chambers. "
+        )
+
+        shock_stimuli = TimeIntervals(name="ShockStimuli", description=description)
+        column_description = "Shock amplitude in mA"
+        shock_stimuli.add_column(name="shock_amplitude", description=column_description)
+        for start_time in shock_times:
+            shock_stimuli.add_interval(
+                start_time=start_time, stop_time=start_time + shock_duration, shock_amplitude=shock_amplitude
+            )
+
+        nwbfile.add_stimulus(shock_stimuli)

src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_all_sessions.py

@@ -95,6 +95,7 @@ def get_session_to_nwb_kwargs_per_session(
     # This can be a specific list with hard-coded sessions, a path expansion or any conversion specific logic that you might need
     #####
     import pandas as pd
+    import re
 
     subjects_df = pd.read_excel(data_dir_path / "Ca_EEG_Design.xlsx")
     subjects = subjects_df["Mouse"]
@@ -104,6 +105,14 @@ def get_session_to_nwb_kwargs_per_session(
         if session_times_file_path.is_file():
             session_times_df = pd.read_csv(session_times_file_path)
             for task in session_times_df["Session"]:
+                if task == "FC":
+                    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(
+                        shock_times=[120.0, 180.0, 240.0], shock_amplitude=shock_amplitude, shock_duration=2.0
+                    )
+                else:
+                    shock_stimulus = None
                 session_id = subject_id + "_" + task
                 session_row = session_times_df[session_times_df["Session"] == task].iloc[0]
                 date_str = session_row["Date"]
@@ -115,6 +124,7 @@ def get_session_to_nwb_kwargs_per_session(
                         session_id=session_id,
                         date_str=date_str,
                         time_str=time_str,
+                        shock_stimulus=shock_stimulus,
                     )
                 )
         else:

src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py

@@ -93,6 +93,7 @@ def session_to_nwb(
     include_sleep_classification: bool = True,
     include_behavioral_video: bool = True,
     include_eeg_emg_signals: bool = True,
+    shock_stimulus: dict = None,
 ):
     print(f"Converting session {session_id}")
     if verbose:
@@ -218,6 +219,14 @@ def session_to_nwb(
     elif verbose and not sleep_classification_file_path.is_file():
         print(f"No sleep classification output csv file found at {sleep_classification_file_path}")
 
+    # Add Shock Stimuli times for FC sessions
+    if shock_stimulus is not None:
+
+        source_data.update(ShockStimuli=dict())
+        conversion_options.update(
+            ShockStimuli=shock_stimulus,
+        )
+
     converter = Zaki2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
@@ -256,7 +265,7 @@ def session_to_nwb(
     # Parameters for conversion
     data_dir_path = Path("D:/")
     subject_id = "Ca_EEG3-4"
-    task = "OfflineDay1Session1"
+    task = "FC"
     session_id = subject_id + "_" + task
     output_dir_path = Path("D:/cai_lab_conversion_nwb/")
     stub_test = False
@@ -265,6 +274,7 @@ def session_to_nwb(
     session_row = df[df["Session"] == task].iloc[0]
     date_str = session_row["Date"]
     time_str = session_row["Time"]
+    shock_stimulus = dict(shock_times=[120.0, 180.0, 240.0], shock_amplitude=0.25, shock_duration=2.0)
     session_to_nwb(
         data_dir_path=data_dir_path,
         output_dir_path=output_dir_path,
@@ -273,4 +283,5 @@ def session_to_nwb(
         session_id=session_id,
         date_str=date_str,
         time_str=time_str,
+        shock_stimulus=shock_stimulus,
     )

src/cai_lab_to_nwb/zaki_2024/zaki_2024_metadata.yaml

@@ -1,44 +1,48 @@
 NWBFile:
   keywords:
     - hippocampus
-    - memory integration
+    - learning
     - memory-linking
     - ensemble
     - reactivation
-    - co-firing
+    - co-activity
     - offline periods
-    - sleep
-    - stress
-    - PTSD
+    - aversive
   related_publications:
-    - https://www.biorxiv.org/content/10.1101/2023.03.13.532469v2
+    - https://doi.org/10.1038/s41586-024-08168-4
   session_description:
-    A rich text description of the experiment. Can also just be the abstract of the publication.
+    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
   institution: Icahn School of Medicine at Mount Sinai
   lab: Cai
   experimenter:
-    - Cai, Denise
-    - Morales-Rodriguez, Denisse
-    - Bacon, Madeline E.
-    - Ko, BumJin
-    - Francisco, Taylor R.
-    - LaBanca, Alexa R.
-    - Sompolpong, Patlapa
-    - Dong, Zhe
-    - Lamsifer, Sophia
-    - Chen, Hung-Tu
-    - Carrillo Segura, Simón
-    - Christenson Wick, Zoé
-    - Silva, Alcino J.
-    - Rajan, Kanaka
-    - van der Meer, Matthijs
-    - Fenton, André
-    - Shuman, Tristan
     - Zaki, Yosif
+  surgery:
+    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.
+  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"
-  sex: U  # One of M, F, U, or O
+  sex: M
 Ophys:
   OnePhotonSeries:
     - name: OnePhotonSeries

src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py

@@ -15,6 +15,7 @@
     Zaki2024SleepClassificationInterface,
     MiniscopeImagingInterface,
     MinianMotionCorrectionInterface,
+    Zaki2024ShockStimuliInterface,
 )
 
 
@@ -30,6 +31,7 @@ class Zaki2024NWBConverter(NWBConverter):
         MultiEDFSignals=Zaki2024MultiEDFInterface,
         FreezingBehavior=EzTrackFreezingBehaviorInterface,
         Video=VideoInterface,
+        ShockStimuli=Zaki2024ShockStimuliInterface,
     )