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).
# === 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]