Metadata Examples

Below, the contents of a fully functioning example metadata file are shown, which contains metadata for several example datasets. This file is included with each installation of neurotic and is loaded automatically when neurotic first starts.

With this metadata file loaded in neurotic, you may use the “Download data” feature to fetch the data files and run the examples, and you may try the “Edit metadata” feature to test modifications (remember to “Reload metadata” after saving changes).

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# ===  GLOBAL PARAMETERS  ======================================================

neurotic_config:
    neurotic_version: '>=1.4' # required for firing_rates

    # the common URL root used for downloading all files
    # - for web browser access to data files, visit
    #   https://gin.g-node.org/jpgill86/neurotic-data/src/master/examples
    remote_data_root: https://gin.g-node.org/jpgill86/neurotic-data/raw/master/examples

# ===  EXAMPLE 1: APLYSIA FEEDING  =============================================

Aplysia feeding:
    description: '[ 13 MB] Sea slug feeding, identified neurons, swallowing force'
    # see also https://gin.g-node.org/jpgill86/neurotic-data/src/master/examples/aplysia-feeding/README.md

    # FILE PATHS
    # - URLs to files are assembled this way:
    #     remote_data_root + remote_data_dir + *_file
    # - downloaded files are stored in a new local directory with name
    #   data_dir created in a location relative to this metadata file
    data_dir:           aplysia-feeding
    remote_data_dir:    aplysia-feeding
    data_file:          data.axgx # AxoGraph file
    video_file:         video.mp4
    annotations_file:   annotations.csv
    epoch_encoder_file: epoch-encoder.csv

    # VIDEO SYNC PARAMETERS
    video_offset: 2875.3 # seconds

    # EPOCH ENCODER PARAMETERS
    epoch_encoder_possible_labels:
        - I2 protraction activity
        - B8 activity
        - B3/6/9/10 activity
        - B38 activity
        - B4/B5 activity
        - Inward movement

    # SIGNAL PLOTTING PARAMETERS
    plots:
        - channel: I2
          ylabel: I2 muscle EMG
          units: uV
          ylim: [-60, 60]
          color: '666666'

        - channel: RN
          ylabel: Radular nerve (RN)
          units: uV
          ylim: [-25, 25]
          color: '666666'

        - channel: BN2
          ylabel: Buccal nerve 2 (BN2)
          units: uV
          ylim: [-45, 45]
          color: '666666'

        - channel: BN3-DIST
          ylabel: Buccal nerve 3 (BN3)
          units: uV
          ylim: [-60, 60]
          color: '666666'

        - channel: Force
          units: mN
          ylim: [-50, 450]
          color: '666666'

    # SIGNAL FILTERS
    # - used here to remove high-frequency noise
    # - only applied if "Fast loading" is turned off (lazy=False)
    filters:
        - channel: I2
          lowpass: 100 # Hz

        - channel: Force
          lowpass: 50 # Hz

    # NEURONAL SPIKE DETECTION
    # - used here to detect activity of identified neurons
    # - only performed if "Fast loading" is turned off (lazy=False)
    amplitude_discriminators:
        - name: B38 neuron
          channel: BN2
          units: uV
          amplitude: [7, 20]
          epoch: B38 activity
          color: 'EFBF46'

        - name: B31/B32/B61/B62 neurons
          channel: I2
          units: uV
          amplitude: [2, 75]
          epoch: I2 protraction activity
          color: 'DC5151'

        - name: B8a/b neurons
          channel: RN
          units: uV
          amplitude: [-30, -8]
          epoch: B8 activity
          color: 'DA8BC3'

        - name: B6/B9 neurons
          channel: BN2
          units: uV
          amplitude: [-25, -9]
          epoch: B3/6/9/10 activity
          color: '64B5CD'

        - name: B3 neuron
          channel: BN2
          units: uV
          amplitude: [-60, -25]
          epoch: B3/6/9/10 activity
          color: '4F80BD'

        - name: B4/B5 neurons
          channel: BN3-DIST
          units: uV
          amplitude: [-80, -20]
          epoch: B4/B5 activity
          color: '00A86B'

    # NEURONAL FIRING RATES
    # - used here to model synaptic output
    # - only calculated if "Fast loading" is turned off (lazy=False)
    firing_rates:
        - name: B38 neuron
          kernel: CausalAlphaKernel
          sigma: 1.0 # seconds

        - name: B6/B9 neurons
          kernel: CausalAlphaKernel
          sigma: 0.5 # seconds

        - name: B3 neuron
          kernel: CausalAlphaKernel
          sigma: 1.0 # seconds

    # NEURONAL BURST DETECTION
    # - used here to classify sequences of spikes into "bursts"
    # - only performed if "Fast loading" is turned off (lazy=False)
    burst_detectors:
        - spiketrain: B38 neuron
          thresholds: [8, 5] # Hz

        - spiketrain: B31/B32/B61/B62 neurons
          thresholds: [10, 5] # Hz

        - spiketrain: B8a/b neurons
          thresholds: [3, 3] # Hz

        - spiketrain: B6/B9 neurons
          thresholds: [10, 5] # Hz

        - spiketrain: B3 neuron
          thresholds: [8, 2] # Hz

        - spiketrain: B4/B5 neurons
          thresholds: [3, 3] # Hz

    # RECTIFIED AND INTEGRATED SIGNALS
    # - only used if "Fast loading" is turned off (lazy=False)
    rauc_bin_duration: 0.1 # seconds


# ===  EXAMPLE 2: HUMAN BALANCE BEAM  ==========================================

Human balance beam:
    description: '[0.5 MB] Narrow beam walking, arm EMG, body kinematics'
    # see also https://gin.g-node.org/jpgill86/neurotic-data/src/master/examples/human-balance-beam/README.md

    # FILE PATHS
    # - URLs to files are assembled this way:
    #     remote_data_root + remote_data_dir + *_file
    # - downloaded files are stored in a new local directory with name
    #   data_dir created in a location relative to this metadata file
    data_dir:           human-balance-beam
    remote_data_dir:    human-balance-beam
    data_file:          data.mat # MATLAB file
    video_file:         video.mp4
    epoch_encoder_file: epoch-encoder.csv

    # VIDEO SYNC PARAMETERS
    video_offset: 0 # seconds

    # INITIAL PLOT WIDTH
    t_width: 10 # seconds

    # EPOCH ENCODER PARAMETERS
    epoch_encoder_possible_labels:
        - Left stance
        - Right stance

    # SIGNAL PLOTTING PARAMETERS
    plots:
        # LEFT ARM
        - channel: Voltage.BCEP_L
          ylabel:  L Biceps
          ylim: [-1, 1]
          units: mV
        - channel: Voltage.TCEP_L
          ylabel:  L Triceps
          ylim: [-1, 1]
          units: mV

        # RIGHT ARM
        - channel: Voltage.BCEP_R
          ylabel:  R Biceps
          ylim: [-10, 10]
          units: mV
        - channel: Voltage.TCEP_R
          ylabel:  R Triceps
          ylim: [-10, 10]
          units: mV

        # KINEMATIC MARKERS
        - channel: CLAV Z
          ylabel:  Clavicle Z
          ylim: [1220, 1420]
        - channel: LHEE Z
          ylabel:  L Heel Z
          ylim: [30, 350]
        - channel: RHEE Z
          ylabel:  R Heel Z
          ylim: [30, 350]

    # SIGNAL FILTERS
    # - used here to remove low-frequency motion artifacts
    # - only applied if "Fast loading" is turned off (lazy=False)
    filters:
        - channel: Voltage.BCEP_R
          highpass: 35 # Hz

        - channel: Voltage.TCEP_R
          highpass: 35 # Hz

    # RECTIFIED AND INTEGRATED SIGNALS
    # - used here to represent overall muscle activity
    # - only used if "Fast loading" is turned off (lazy=False)
    rauc_baseline: mean     # subtract the mean before rectification
    rauc_bin_duration: 0.01 # seconds


# ===  EXAMPLE 3: DRONE OPTICAL FLOW  ==========================================

Drone optical flow:
    description: '[7.7 MB] Neural network motion detection from drone flight video'
    # see also https://gin.g-node.org/jpgill86/neurotic-data/src/master/examples/drone-optical-flow/README.md

    # FILE PATHS
    # - URLs to files are assembled this way:
    #     remote_data_root + remote_data_dir + *_file
    # - downloaded files are stored in a new local directory with name
    #   data_dir created in a location relative to this metadata file
    data_dir:           drone-optical-flow
    remote_data_dir:    drone-optical-flow
    data_file:          data.txt # plain text file
    video_file:         video.mp4

    # DATA READER (NEO) PARAMETERS
    # - these arguments are passed to a Neo reader (neo.io.AsciiSignalIO) for
    #   reading the data_file
    io_args:
        skiprows: 1 # skip header
        sampling_rate: 1250 # Hz
        units: mV

    # VIDEO SYNC PARAMETERS
    video_offset: 0 # seconds

    # SIGNAL PLOTTING PARAMETERS
    plots:
        - channel: Column 0
          ylabel: Clockwise Rotate
          units: mV
          ylim: [0, 255]

        - channel: Column 1
          ylabel: Counterclockwise Rotate
          units: mV
          ylim: [0, 255]

        - channel: Column 2
          ylabel: Moving Forward
          units: mV
          ylim: [0, 255]

        - channel: Column 3
          ylabel: Moving Backward
          units: mV
          ylim: [0, 255]

        - channel: Column 4
          ylabel: Down Shift
          units: mV
          ylim: [0, 255]

        - channel: Column 5
          ylabel: Up Shift
          units: mV
          ylim: [0, 255]

        - channel: Column 6
          ylabel: Right Shift
          units: mV
          ylim: [0, 255]

        - channel: Column 7
          ylabel: Left Shift
          units: mV
          ylim: [0, 255]

    # NEURONAL SPIKE DETECTION
    # - used here to detect spikes of simulated neurons
    # - only performed if "Fast loading" is turned off (lazy=False)
    amplitude_discriminators:
        - name: Clockwise Rotate
          channel: Column 0
          units: mV
          amplitude: [150, 255]

        - name: Counterclockwise Rotate
          channel: Column 1
          units: mV
          amplitude: [150, 255]

        - name: Moving Forward
          channel: Column 2
          units: mV
          amplitude: [150, 255]

        - name: Moving Backward
          channel: Column 3
          units: mV
          amplitude: [150, 255]

        - name: Down Shift
          channel: Column 4
          units: mV
          amplitude: [150, 255]

        - name: Up Shift
          channel: Column 5
          units: mV
          amplitude: [150, 255]

        - name: Right Shift
          channel: Column 6
          units: mV
          amplitude: [150, 255]

        - name: Left Shift
          channel: Column 7
          units: mV
          amplitude: [150, 255]