# === 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]