# install cell skipped during CI (deps preinstalled into system Python)

# Core data manipulation and analysis
from pathlib import Path

import h5py

# Visualization
import matplotlib.pyplot as plt
import remfile
from dandi.dandiapi import DandiAPIClient

# NWB and DANDI access
from pynwb import NWBHDF5IO

# Configure matplotlib
plt.rcParams['figure.figsize'] = (12, 6)
plt.rcParams['font.size'] = 10

def load_nwb_from_dandi(dandiset_id, subject_id, session_id):
    """
    Load NWB file from DANDI Archive via streaming.
    """
    pattern = f"sub-{subject_id}/sub-{subject_id}_ses-{session_id}*.nwb"
    
    with DandiAPIClient() as client:
        assets = client.get_dandiset(dandiset_id, "draft").get_assets_by_glob(
            pattern=pattern, order="path"
        )
        
        s3_urls = []
        for asset in assets:
            s3_url = asset.get_content_url(follow_redirects=1, strip_query=False)
            s3_urls.append(s3_url)
        
        if len(s3_urls) != 1:
            raise ValueError(f"Expected 1 file, found {len(s3_urls)} for pattern {pattern}")
        
        s3_url = s3_urls[0]
    
    file = remfile.File(s3_url)
    h5_file = h5py.File(file, "r")
    io = NWBHDF5IO(file=h5_file, load_namespaces=True)
    nwbfile = io.read()
    
    return nwbfile, io


def load_nwb_local(directory_path, subject_id, session_id):
    """
    Load NWB file from local directory.
    """
    directory_path = Path(directory_path)
    nwbfile_path = directory_path / f"sub-{subject_id}_ses-{session_id}.nwb"
    
    if not nwbfile_path.exists():
        raise FileNotFoundError(f"NWB file not found: {nwbfile_path}")
    
    io = NWBHDF5IO(path=nwbfile_path, load_namespaces=True)
    nwbfile = io.read()
    
    return nwbfile, io

# Load session data
dandiset_id = "001528"
subject_id = "C4561"  # Example subject
session_id = "varying-duration"  # Start with first session type

# Choose data source (DANDI streaming or local)
USE_DANDI = True  # Set to False to use local files

if USE_DANDI:
    nwbfile, io = load_nwb_from_dandi(dandiset_id, subject_id, session_id)
else:
    # Specify your local directory path
    local_directory = "YOUR_DIRECTORY_PATH"  # Replace with actual path
    nwbfile, io = load_nwb_local(local_directory, subject_id, session_id)

print("=== SESSION INFORMATION ===")
print(f"Experiment description:\n {nwbfile.experiment_description}")
print(f"Session description:\n {nwbfile.session_description}")
print(f"Session start time:\n {nwbfile.session_start_time}")

=== SESSION INFORMATION ===
Experiment description:
 SNr GABAergic neurons recordings. Mice were freely moving on a plastic tub. Simultaneous passive optogenetic stimulation and fiber photometry recordings were conducted during the first two days. Excitatory inputs from either the STN or PPN to SN were stimulated. Recordings of GCaMP6f fluorescence signal captured pan-GABA activity in the SNr in VGLUT2-Cre x VGAT-Flp mice.
Session description:
 The subject is placed in a plastic tub and is recorded for 3.5 minutes. The subject receives a 40 Hz stimulation at various durations (i.e. 250ms, 1s and 4s) 5 times for each duration) with an inter-stimulus interval (ISI) of 10s. 
Session start time:
 2024-01-18 10:24:56-00:01

print("=== SUBJECT INFORMATION ===")
print(f"ID: {nwbfile.subject.subject_id}")
print(f"Age: {nwbfile.subject.age}")
print(f"Strain: {nwbfile.subject.species}")
print(f"Genotype: {nwbfile.subject.genotype}")
print(f"Sex: {nwbfile.subject.sex}")

=== SUBJECT INFORMATION ===
ID: C4561
Age: P6W
Strain: Mus musculus
Genotype: VGlut2-cre x VGAT-flp
Sex: F

print("=== FIBER PHOTOMETRY METADATA ===")
print("All fiber photometry metadata are stored in the fiber_photometry module in lab_meta_data:")
nwbfile.lab_meta_data["fiber_photometry"]

=== FIBER PHOTOMETRY METADATA ===
All fiber photometry metadata are stored in the fiber_photometry module in lab_meta_data:

print("=== FP SETUP INFORMATION ===")
print("Components used in fiber photometry setup:")
for key in nwbfile.devices.keys():
    if "BehavioralCamera" in key or "optogenetic" in key:
        continue
    print(key)

=== FP SETUP INFORMATION ===
Components used in fiber photometry setup:
dichroic_mirror
emission_filter
excitation_filter
excitation_source_calcium_signal
excitation_source_isosbestic_control
optical_fiber_SNr
photodetector

nwbfile.devices["excitation_source_calcium_signal"]

nwbfile.devices["excitation_source_calcium_signal"]

nwbfile.devices["excitation_filter"]

nwbfile.devices["emission_filter"]

nwbfile.devices["dichroic_mirror"]

nwbfile.devices["photodetector"]

for key in nwbfile.devices.keys():
    if "optical_fiber" in key:
        optical_fiber = nwbfile.devices[key]
optical_fiber

print("=== FLUORESCENT CALCIUM SENSOR ===")
print("Fluorescent calcium sensor used in this experiment:")
nwbfile.lab_meta_data["fiber_photometry"].fiber_photometry_indicators

=== FLUORESCENT CALCIUM SENSOR ===
Fluorescent calcium sensor used in this experiment:

print("=== ACQUISITION MODULE ===\n")
for name, acq in nwbfile.acquisition.items():
    print(f"{name} - {acq.description}")
    if "raw_signal" in name:
        raw_signal_series_name = name

=== ACQUISITION MODULE ===

BehavioralVideo - Video recording of the mouse's behavior. Recorded using a camera mounted on the ceiling above the chambers.

raw_signal_SNr - The raw modulated fluorescence signal from GCaMP6f calcium indicator in SNr GABAergic neurons, excited at 465nm and 405nm, respectively.

# Access raw fiber photometry data
raw_signal = nwbfile.acquisition[raw_signal_series_name]

print("=== RAW FIBER PHOTOMETRY SIGNAL ===")
print(f"Name: {raw_signal.name}")
print(f"Description: {raw_signal.description}")
print(f"Data shape: {raw_signal.data.shape}")
print(f"Sampling rate: {raw_signal.rate} Hz")
print(f"Duration: {raw_signal.data.shape[0] / raw_signal.rate:.2f} seconds")

=== RAW FIBER PHOTOMETRY SIGNAL ===
Name: raw_signal_SNr
Description: The raw modulated fluorescence signal from GCaMP6f calcium indicator in SNr GABAergic neurons, excited at 465nm and 405nm, respectively.
Data shape: (1580544,)
Sampling rate: 6103.515625 Hz
Duration: 258.96 seconds

nwbfile.acquisition[raw_signal_series_name]

# Plot raw acquisition signal (simple view)
data = raw_signal.data[:]
timestamps = raw_signal.get_timestamps()

# Show first 30 seconds
end_idx = int(30 * raw_signal.rate)
time_subset = timestamps[:end_idx]
data_subset = data[:end_idx]

plt.figure(figsize=(15, 2))
plt.plot(time_subset, data_subset, linewidth=0.5)
plt.xlabel('Time (s)')
plt.ylabel('Fluorescence (a.u.)')
plt.title('Raw Modulated Fiber Photometry Signal (first 30 seconds)')
plt.grid(True, alpha=0.3)
plt.show()

print("=== OPHYS PROCESSING MODULE ===")
processed_fp = nwbfile.processing["ophys"]
print(processed_fp.description, "\n")
for name, fp in processed_fp.items():
    print("-"*20)
    print(f"Name: {fp.name}")
    print(f"Description: {fp.description}")
    print(f"Sampling rate: {fp.rate} Hz")
    print(f"Metadata:")
    fp_metadata = fp.fiber_photometry_table_region[:]
    print(f"  Location: {fp_metadata['location'].values[0]}")
    print(f"  Excitation wavelength: {fp_metadata['excitation_wavelength_in_nm'].values[0]} nm")

=== OPHYS PROCESSING MODULE ===
Processed fiber photometry signals 

--------------------
Name: deltaF_over_F_SNr
Description: The deltaF/F signal from GCaMP6f calcium indicator in SNr GABAergic neurons, excited at 465nm and calculated as (Gc - fitted_af) / fitted_af.
Sampling rate: 100.0 Hz
Metadata:
  Location: SNr
  Excitation wavelength: 465.0 nm
--------------------
Name: demodulated_calcium_signal_SNr
Description: The demodulated fluorescence signal from GCaMP6f calcium indicator in SNr GABAergic neurons, excited at 465nm and demodulated at 330Hz.
Sampling rate: 6103.5156 Hz
Metadata:
  Location: SNr
  Excitation wavelength: 465.0 nm
--------------------
Name: demodulated_isosbestic_control_SNr
Description: The demodulated fluorescence signal from GCaMP6f for isosbestic control in SNr GABAergic neurons, excited at 405nm and demodulated at 210Hz.
Sampling rate: 6103.5156 Hz
Metadata:
  Location: SNr
  Excitation wavelength: 405.0 nm
--------------------
Name: downsampled_calcium_signal_SNr
Description: The downsampled fluorescence signal from GCaMP6f calcium indicator in SNr GABAergic neurons, excited at 465nm and downsampled at 100Hz.
Sampling rate: 100.0 Hz
Metadata:
  Location: SNr
  Excitation wavelength: 465.0 nm
--------------------
Name: downsampled_isosbestic_control_SNr
Description: The downsampled fluorescence signal from GCaMP6f for isosbestic control in SNr GABAergic neurons, excited at 405nm and downsampled at 100Hz.
Sampling rate: 100.0 Hz
Metadata:
  Location: SNr
  Excitation wavelength: 405.0 nm

# Access behavioral video information
if "BehavioralVideo" in nwbfile.acquisition:
    video = nwbfile.acquisition["BehavioralVideo"]

    print("=== BEHAVIORAL VIDEO ===")
    print(f"Video file path: {video.external_file[0]}")
    print(f"Description: {video.description}")
    print(f"Video start: {video.timestamps[0]} seconds")
    print(f"Video end: {video.timestamps[-1]} seconds")
else:
    print("No behavioral video found in this session.")

=== BEHAVIORAL VIDEO ===
Video file path: sub-C4561_ses-varying-durations_image\5edc8957-c811-4c13-bc52-491745c3f527_external_file_0.mp4
Description: Video recording of the mouse's behavior. Recorded using a camera mounted on the ceiling above the chambers.

Video start: 39.0 seconds
Video end: 249.001 seconds

video.device  # Display video device information

print("=== OPTOGENETIC STIMULUS METADATA ===")
print("All optogenetic stimulus metadata are stored in the optogenetic_experiment_metadata module in lab_meta_data:")
nwbfile.lab_meta_data["optogenetic_experiment_metadata"]

=== OPTOGENETIC STIMULUS METADATA ===
All optogenetic stimulus metadata are stored in the optogenetic_experiment_metadata module in lab_meta_data:

print("=== OPTOGENETIC SETUP INFORMATION ===")
print("Components used in optogenetic setup:")
for key in nwbfile.devices.keys():
    if "optogenetic" in key:
        print(key)

=== OPTOGENETIC SETUP INFORMATION ===
Components used in optogenetic setup:
optogenetic_excitation_source

nwbfile.devices["optogenetic_excitation_source"]

print("=== OPSIN ===")
print("Opsin used in this experiment:")
nwbfile.lab_meta_data["optogenetic_experiment_metadata"].optogenetic_effectors

=== OPSIN ===
Opsin used in this experiment:

# Access optogenetic stimulation data
ogen_df = nwbfile.intervals["optogenetic_epochs_table"].to_dataframe()

print("=== OPTOGENETIC STIMULATION INTERVALS ===")
print(f"Total number of stimuli: {len(ogen_df)}")
print("\nFirst 5 intervals:")
ogen_df.head()

=== OPTOGENETIC STIMULATION INTERVALS ===
Total number of stimuli: 15

First 5 intervals:

# Plot optogenetic stimulation and demodulated signal together
fig, ax = plt.subplots(1, 1, figsize=(14, 6))

# Plot demodulated calcium signal
for name, fp in processed_fp.items():
    if "downsampled_calcium" in name:
        calcium_signal = fp
    elif "downsampled_isosbestic" in name:
        isosbestic_signal = fp

calcium_data = calcium_signal.data[:]
isosbestic_data = isosbestic_signal.data[:]
timestamps = calcium_signal.get_timestamps()
ax.plot(timestamps, calcium_data, color="blue", linewidth=0.8, alpha=0.8, label="Calcium Signal")
ax.plot(timestamps, isosbestic_data, color="red", linewidth=0.8, alpha=0.6, label="Isosbestic Signal")
ax.set_xlabel('Time (s)')
ax.set_ylabel('Downsampled Signal (a.u.)')
ax.set_title('Calcium Signal / Isosbestic Control with Optogenetic Stimulation (40 Hz, Varying Duration)')
ax.grid(True, alpha=0.3)
ax.legend()

# Add stimulus intervals as faded boxes over the signal
duration_colors = {0.25: 'red', 1.0: 'blue', 4.0: 'green'}
duration_labels = {0.25: "250ms stimulus", 1.0: "1s stimulus", 4.0: "4s stimulus"}

for i, row in ogen_df.iterrows():
    duration = row['stop_time'] - row['start_time']
    # Round duration to nearest expected value for color mapping
    rounded_duration = round(duration * 4) / 4  # Round to nearest 0.25
    color = duration_colors.get(rounded_duration, 'gray')
    ax.axvspan(
        row["start_time"],
        row["stop_time"],
        color=color,
        alpha=0.2,
        label=duration_labels.get(rounded_duration, f"{rounded_duration}s"),
    )
    # Remove duplicate legend entries
    handles, labels = ax.get_legend_handles_labels()
    by_label = dict(zip(labels, handles))
    ax.legend(by_label.values(), by_label.keys())
plt.tight_layout()
plt.show()

# Load varying frequency session
session_id_freq = "varying-frequencies"

if USE_DANDI:
    nwbfile_freq, io_freq = load_nwb_from_dandi(dandiset_id, subject_id, session_id_freq)
else:
    nwbfile_freq, io_freq = load_nwb_local(local_directory, subject_id, session_id_freq)

print("=== SESSION INFORMATION ===")
print(f"Experiment description:\n {nwbfile_freq.experiment_description}")
print(f"Session description:\n {nwbfile_freq.session_description}")
print(f"Session start time:\n {nwbfile_freq.session_start_time}")

=== SESSION INFORMATION ===
Experiment description:
 SNr GABAergic neurons recordings. Mice were freely moving on a plastic tub. Simultaneous passive optogenetic stimulation and fiber photometry recordings were conducted during the first two days. Excitatory inputs from either the STN or PPN to SN were stimulated. Recordings of GCaMP6f fluorescence signal captured pan-GABA activity in the SNr in VGLUT2-Cre x VGAT-Flp mice.
Session description:
 The subject is placed in a plastic tub and undergoes 3 recording sessions corresponding to a fixed duration of stimulation (i.e., 250ms, 1s, and 4s). Each session lasted 8 minutes. The subject receives optogenetic stimulation at varying frequencies (5 Hz, 10 Hz , 20 Hz and 40 Hz) 5 times for each duration with an ISI of 10s. 
Session start time:
 2024-01-17 16:33:47-00:01

trials_freq_df = nwbfile_freq.trials.to_dataframe()
print("=== TRIALS TABLE ===")
print(f"Total number of trials: {len(trials_freq_df)}")
trials_freq_df

=== TRIALS TABLE ===
Total number of trials: 3

# Access optogenetic stimulation data
ogen_df = nwbfile_freq.intervals["optogenetic_epochs_table"].to_dataframe()

print("=== OPTOGENETIC STIMULATION INTERVALS ===")
print(f"Total number of stimuli: {len(ogen_df)}")
print("\nFirst 5 intervals:")
ogen_df.head()

=== OPTOGENETIC STIMULATION INTERVALS ===
Total number of stimuli: 60

First 5 intervals:

# Plot optogenetic stimulation and demodulated signal together
fig, axs = plt.subplots(3, 1, figsize=(14, 6))
# Plot demodulated calcium signal
processed_fp = nwbfile_freq.processing["ophys"]
for name, fp in processed_fp.items():
    if "downsampled_calcium" in name:
        calcium_signal = fp
    elif "downsampled_isosbestic" in name:
        isosbestic_signal = fp

calcium_data_freq = calcium_signal.data[:]
isosbestic_data_freq = isosbestic_signal.data[:]
timestamps_freq = calcium_signal.get_timestamps()

# Plot first trial
for i in range(3):
    trial_start_time = trials_freq_df.iloc[i]["start_time"]
    trial_end_time = trials_freq_df.iloc[i]["stop_time"]
    tag = trials_freq_df.iloc[i]["tags"]
    timestamps = timestamps_freq[(timestamps_freq >= trial_start_time) & (timestamps_freq <= trial_end_time)]
    calcium_data = calcium_data_freq[(timestamps_freq >= trial_start_time) & (timestamps_freq <= trial_end_time)]
    isosbestic_data = isosbestic_data_freq[(timestamps_freq >= trial_start_time) & (timestamps_freq <= trial_end_time)]
    # Plot demodulated calcium signal
    axs[i].plot(timestamps, calcium_data, color="blue", linewidth=0.8, alpha=0.8, label="Calcium Signal")
    axs[i].plot(timestamps, isosbestic_data, color="red", linewidth=0.8, alpha=0.6, label="Isosbestic Signal")
    axs[i].set_xlabel("Time (s)")
    axs[i].set_ylabel("Downsampled Signal (a.u.)")
    axs[i].set_title(f"Calcium Signal / Isosbestic Signal with Optogenetic Stimulation ({tag}, Varying Frequencies)")
    axs[i].grid(True, alpha=0.3)

    # Add stimulus intervals as faded boxes over the signal
    frequency_colors = {5.0: "red", 10.0: "blue", 20.0: "green", 40.0: "yellow"}
    frequency_labels = {5.0: "5Hz stimulus", 10.0: "10Hz stimulus", 20.0: "20Hz stimulus", 40.0: "40Hz stimulus"}

    for r, row in ogen_df.iterrows():
        # select rows within the trial time
        if not (row["start_time"] >= trial_start_time and row["stop_time"] <= trial_end_time):
            continue
        frequency = row["stimulus_frequency"]
        color = frequency_colors.get(frequency, "gray")
        axs[i].axvspan(
            row["start_time"],
            row["stop_time"],
            color=color,
            alpha=0.2,
            label=frequency_labels.get(frequency, f"{frequency}Hz"),
        )

    handles, labels = axs[i].get_legend_handles_labels()
    by_label = dict(zip(labels, handles))
    axs[0].legend(by_label.values(), by_label.keys())

plt.tight_layout()
plt.show()

	location	excitation_wavelength_in_nm	emission_wavelength_in_nm	indicator	optical_fiber	excitation_source	photodetector	dichroic_mirror	emission_filter	excitation_filter
id
0	SNr	465.0	515.0	GCaMP6f_SNr abc.Indicator at 0x140528600291312\nFields:\n description: GCaMP6f calcium sensor in SNr GABAergic neurons\n label: GCaMP6f\n manufacturer: Addgene\n viral_vector_injection: viral_vector_injection_SNr abc.ViralVectorInjection at 0x140528600290976\nFields:\n ap_in_mm: -3.3\n description: Viral injection of GCaMP6f in SNr.\n dv_in_mm: -4.6\n hemisphere: left\n location: SNr\n ml_in_mm: -1.3\n reference: bregma at the cortical surface\n viral_vector: viral_vector_gcamp6f abc.ViralVector at 0x140528600289968\nFields:\n construct_name: AAV1-Ef1a-fDIO-GCaMP6f\n description: AAV1 viral vector expressing GCaMP6f calcium sensor under EF1a promoter for fiber photometry recording in SNr\n manufacturer: Addgene (catalog number 1283125)\n titer_in_vg_per_ml: 4000000000000.0\n\n volume_in_uL: 0.3\n\n	optical_fiber_SNr abc.OpticalFiber at 0x140528600298704\nFields:\n description: Chronically implanted optic fiber.\n fiber_insertion: fiber_insertion abc.FiberInsertion at 0x140528600298368\nFields:\n hemisphere: left\n insertion_position_ap_in_mm: -3.3\n insertion_position_dv_in_mm: -4.4\n insertion_position_ml_in_mm: -1.4\n position_reference: bregma\n\n model: optical_fiber_model_1 abc.OpticalFiberModel at 0x140528600298032\nFields:\n active_length_in_mm: 6.0\n core_diameter_in_um: 400.0\n description: Chronically implantable optic fiber.\n ferrule_diameter_in_mm: 1.25\n ferrule_name: black ceramic ferrule\n manufacturer: RWD\n model_number: <model of the optical fiber>\n numerical_aperture: 0.39\n\n serial_number: <serial number of the optical fiber>\n	excitation_source_calcium_signal abc.ExcitationSource at 0x140528600297696\nFields:\n description: excitation source for the sensor's fluorescence signal (465nm) modulated at 210 Hz.\n model: excitation_source_model_calcium abc.ExcitationSourceModel at 0x140528600297360\nFields:\n description: excitation source for GCaMP6f sensor.\n excitation_mode: one-photon\n manufacturer: Tucker-Davis Technologies\n model_number: RZ5P or RZ10x\n source_type: LED\n wavelength_range_in_nm: [460. 490.]\n\n	photodetector abc.Photodetector at 0x140528600299376\nFields:\n description: <description of the photodetector>\n model: photodetector_model abc.PhotodetectorModel at 0x140528600299040\nFields:\n description: <description of the photodetector model>\n detector_type: Silicon photodiode\n gain: 0.38\n gain_unit: A/W\n manufacturer: <manufacturer of the photodetector>\n model_number: <model of the photodetector>\n wavelength_range_in_nm: [500. 540.]\n\n serial_number: <serial number of the photodetector>\n	dichroic_mirror abc.DichroicMirror at 0x140528600296352\nFields:\n description: dichroic mirror for GCaMP6f fluorescence signal.\n model: dichroic_mirror_model abc.DichroicMirrorModel at 0x140528600296016\nFields:\n description: dichroic mirror model for GCaMP6f fluorescence signal.\n manufacturer: <manufacturer of the dichroic mirror>\n model_number: <model of the dichroic mirror>\n\n serial_number: <serial number of the dichroic mirror>\n	emission_filter abc.BandOpticalFilter at 0x140528600297024\nFields:\n description: emission filter for GCaMP6f fluorescence signal.\n model: emission_filter_model abc.BandOpticalFilterModel at 0x140528600296688\nFields:\n bandwidth_in_nm: 40.0\n center_wavelength_in_nm: 520.0\n description: emission filter model for GCaMP6f fluorescence signal.\n filter_type: Bandpass\n manufacturer: <manufacturer of the emission filter>\n model_number: <model of the emission filter>\n\n	excitation_filter abc.BandOpticalFilter at 0x140528611694928\nFields:\n description: excitation filter for GCaMP6f fluorescence signal.\n model: excitation_filter_model abc.BandOpticalFilterModel at 0x140528611694608\nFields:\n bandwidth_in_nm: 90.0\n center_wavelength_in_nm: 445.0\n description: excitation filter model for GCaMP6f fluorescence signal.\n filter_type: Bandpass\n manufacturer: <manufacturer of the excitation filter>\n model_number: <model of the excitation filter>\n\n
1	SNr	405.0	515.0	GCaMP6f_SNr abc.Indicator at 0x140528600291312\nFields:\n description: GCaMP6f calcium sensor in SNr GABAergic neurons\n label: GCaMP6f\n manufacturer: Addgene\n viral_vector_injection: viral_vector_injection_SNr abc.ViralVectorInjection at 0x140528600290976\nFields:\n ap_in_mm: -3.3\n description: Viral injection of GCaMP6f in SNr.\n dv_in_mm: -4.6\n hemisphere: left\n location: SNr\n ml_in_mm: -1.3\n reference: bregma at the cortical surface\n viral_vector: viral_vector_gcamp6f abc.ViralVector at 0x140528600289968\nFields:\n construct_name: AAV1-Ef1a-fDIO-GCaMP6f\n description: AAV1 viral vector expressing GCaMP6f calcium sensor under EF1a promoter for fiber photometry recording in SNr\n manufacturer: Addgene (catalog number 1283125)\n titer_in_vg_per_ml: 4000000000000.0\n\n volume_in_uL: 0.3\n\n	optical_fiber_SNr abc.OpticalFiber at 0x140528600298704\nFields:\n description: Chronically implanted optic fiber.\n fiber_insertion: fiber_insertion abc.FiberInsertion at 0x140528600298368\nFields:\n hemisphere: left\n insertion_position_ap_in_mm: -3.3\n insertion_position_dv_in_mm: -4.4\n insertion_position_ml_in_mm: -1.4\n position_reference: bregma\n\n model: optical_fiber_model_1 abc.OpticalFiberModel at 0x140528600298032\nFields:\n active_length_in_mm: 6.0\n core_diameter_in_um: 400.0\n description: Chronically implantable optic fiber.\n ferrule_diameter_in_mm: 1.25\n ferrule_name: black ceramic ferrule\n manufacturer: RWD\n model_number: <model of the optical fiber>\n numerical_aperture: 0.39\n\n serial_number: <serial number of the optical fiber>\n	excitation_source_isosbestic_control abc.ExcitationSource at 0x140528611695888\nFields:\n description: excitation source for the sensor's isosbestic control (405nm) modulated at 330 Hz.\n model: excitation_source_model_isosbestic abc.ExcitationSourceModel at 0x140528611695568\nFields:\n description: excitation source for GCaMP6f sensor's isosbestic control.\n excitation_mode: one-photon\n manufacturer: Tucker-Davis Technologies\n model_number: RZ5P or RZ10x\n source_type: LED\n wavelength_range_in_nm: [400. 410.]\n\n	photodetector abc.Photodetector at 0x140528600299376\nFields:\n description: <description of the photodetector>\n model: photodetector_model abc.PhotodetectorModel at 0x140528600299040\nFields:\n description: <description of the photodetector model>\n detector_type: Silicon photodiode\n gain: 0.38\n gain_unit: A/W\n manufacturer: <manufacturer of the photodetector>\n model_number: <model of the photodetector>\n wavelength_range_in_nm: [500. 540.]\n\n serial_number: <serial number of the photodetector>\n	dichroic_mirror abc.DichroicMirror at 0x140528600296352\nFields:\n description: dichroic mirror for GCaMP6f fluorescence signal.\n model: dichroic_mirror_model abc.DichroicMirrorModel at 0x140528600296016\nFields:\n description: dichroic mirror model for GCaMP6f fluorescence signal.\n manufacturer: <manufacturer of the dichroic mirror>\n model_number: <model of the dichroic mirror>\n\n serial_number: <serial number of the dichroic mirror>\n	emission_filter abc.BandOpticalFilter at 0x140528600297024\nFields:\n description: emission filter for GCaMP6f fluorescence signal.\n model: emission_filter_model abc.BandOpticalFilterModel at 0x140528600296688\nFields:\n bandwidth_in_nm: 40.0\n center_wavelength_in_nm: 520.0\n description: emission filter model for GCaMP6f fluorescence signal.\n filter_type: Bandpass\n manufacturer: <manufacturer of the emission filter>\n model_number: <model of the emission filter>\n\n	excitation_filter abc.BandOpticalFilter at 0x140528611694928\nFields:\n description: excitation filter for GCaMP6f fluorescence signal.\n model: excitation_filter_model abc.BandOpticalFilterModel at 0x140528611694608\nFields:\n bandwidth_in_nm: 90.0\n center_wavelength_in_nm: 445.0\n description: excitation filter model for GCaMP6f fluorescence signal.\n filter_type: Bandpass\n manufacturer: <manufacturer of the excitation filter>\n model_number: <model of the excitation filter>\n\n

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Shape	(2,)
Array size	16.00 bytes

Data type	float64
Shape	(2,)
Array size	16.00 bytes

Data type	float64
Shape	(2,)
Array size	16.00 bytes

Data type	float32
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Chunk shape	(1580544,)
Compression	gzip
Compression opts	4
Uncompressed size (bytes)	6322176
Compressed size (bytes)	3137504
Compression ratio	2.015033606331657

Installing requirements¶

Fiber photometry of SNc/SNr dopamine and GABA neuron responses to optogenetic STN and PPN stimulation in Parkinson's disease¶

Study Overview¶

Contents¶

1. Setup and Data Access ¶

Import Required Libraries¶

Data Access Functions¶

2. Session and Subject Metadata ¶

3. Fiber Photometry Data and Metadata ¶

Fiber Photometry Metadata¶

fiber_photometry (FiberPhotometry)

excitation_source_calcium_signal (ExcitationSource)

excitation_source_calcium_signal (ExcitationSource)

excitation_filter (BandOpticalFilter)

emission_filter (BandOpticalFilter)

dichroic_mirror (DichroicMirror)

photodetector (Photodetector)

optical_fiber_SNr (OpticalFiber)

fiber_photometry_indicators (FiberPhotometryIndicators)

Raw (modulated) FiberPhotometry Series¶

raw_signal_SNr (FiberPhotometryResponseSeries)

Processed FiberPhotometry Series¶

Behavioral Video¶

BehavioralCamera (Device)

4. Optogenetic Stimulus and Metadata ¶

Optogenetic Metadata¶

optogenetic_experiment_metadata (OptogeneticExperimentMetadata)

optogenetic_excitation_source (ExcitationSource)

optogenetic_effectors (OptogeneticEffectors)

Optogenetic Stimulus Data¶

5. Session Type 1: Varying Duration Optogenetic Stimulation ¶

6. Session Type 2: Varying Frequency Optogenetic Stimulation ¶

Access trial table¶

Access optogenetic stimulus¶

Access processed fiber photometry signal¶

	effector	excitation_source
id
0	chrimsonR_PPN abc.Effector at 0x140528600294672\nFields:\n description: ChrimsonR opsin used for optogenetic stimulation injected into the PPN.\n label: ChrimsonR-tdTomato\n manufacturer: Addgene\n viral_vector_injection: viral_vector_injection_PPN abc.ViralVectorInjection at 0x140528611693328\nFields:\n ap_in_mm: -4.48\n description: Viral injection into the Pedunculopontine Nucleus (PPN).\n dv_in_mm: -3.75\n hemisphere: left\n location: PPN\n ml_in_mm: -1.1\n reference: bregma at the cortical surface\n viral_vector: viral_vector_ogen abc.ViralVector at 0x140528611693008\nFields:\n construct_name: pAAV-Syn-FLEX-rc[ChrimsonR-tdTomato] (AAV5)\n description: pAAV-Syn-FLEX-rc[ChrimsonR-tdTomato] (AAV5) viral vector was used for optogenetic experiments.\n manufacturer: Addgene (catalog number 62723)\n titer_in_vg_per_ml: 4000000000000.0\n\n volume_in_uL: 0.15\n\n	optogenetic_excitation_source abc.ExcitationSource at 0x140528611696528\nFields:\n description: Red LED device used for optogenetic stimulation.\n model: optogenetic_excitation_source_model abc.ExcitationSourceModel at 0x140528611696208\nFields:\n description: Red LED device used for optogenetic stimulation.\n excitation_mode: one-photon\n manufacturer: Shanghai laser\n model_number: <model of the LED device>\n source_type: LED\n wavelength_range_in_nm: [580. 680.]\n\n

	start_time	stop_time	stimulation_on	pulse_length_in_ms	period_in_ms	number_pulses_per_pulse_train	number_trains	intertrain_interval_in_ms	power_in_mW	wavelength_in_nm	optogenetic_sites	stimulus_frequency
id
0	64.586711	65.585480	True	1.0	25.0	39	1	0.0	5.0	635.0	e...	40.0
1	100.585964	101.584896	True	1.0	25.0	39	1	0.0	5.0	635.0	e...	40.0
2	136.635023	137.635922	True	1.0	25.0	40	1	0.0	5.0	635.0	e...	40.0
3	172.720456	173.720044	True	1.0	25.0	39	1	0.0	5.0	635.0	e...	40.0
4	208.785244	209.785487	True	1.0	25.0	40	1	0.0	5.0	635.0	e...	40.0

	start_time	stop_time	tags
id
0	679.0	1134.024995	[1s]
1	34.0	474.005010	[250ms]
2	1268.0	1783.031035	[4s]

	start_time	stop_time	stimulation_on	pulse_length_in_ms	period_in_ms	number_pulses_per_pulse_train	number_trains	intertrain_interval_in_ms	power_in_mW	wavelength_in_nm	optogenetic_sites	stimulus_frequency
id
0	74.955981	75.206001	True	1.0	100.0	2	1	0.0	5.0	635.0	e...	10.0
1	155.955200	156.204728	True	1.0	100.0	2	1	0.0	5.0	635.0	e...	10.0
2	236.954092	237.203620	True	1.0	100.0	2	1	0.0	5.0	635.0	e...	10.0
3	318.003446	318.254612	True	1.0	100.0	2	1	0.0	5.0	635.0	e...	10.0
4	399.003320	399.253012	True	1.0	100.0	2	1	0.0	5.0	635.0	e...	10.0