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params.yaml
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---
#########################
# Simulation parameters #
#########################
"simulation":
"unit": 0.5 # The minimum unit of simulation (micromters)
# smaller value can burden process and memory
########################
# RECORDING parameters #
########################
# General parameters
"NIDs": 6396 # Total number of neurons
# It is automatically set on calcium imaging mode
# Recording parameters:
"recording":
"recording_time": 4 # Recording time (seconds)
"frame_rate": 120 # Frame rate (Hz)
"mode": "decimation" # one of ["binning", "decimation"]
"gaussian_noise": 0.05 # standard deviation of Gaussian noise
"shot_noise": 0.05 # (underdevelopment) Poisson noise
"microscopy": "LSM" # one of ["raw", "LSM"(underdevelopment), "LFM"(underdevelopment), "XLFM"(underdevelopment)]
# "raw": original calcium signal itself
# "LSM": Light Sheet Microscopy
# "LFM": Light Field Microscopy
# "XLFM": eXtended field of view LFM
"z_depth": 100 # depth of focal plane (micrometer) (underdevelopment)
"pixel_size": 0.8 # pixel size of a camera (micrometer) (underdevelopment)
"FOV": [256, 256] # field of view of a camera (pixels) (underdevelopment)
# can be 2d or 3d
# Physiological parameters:
"physiological":
"refractory_period": 1000 # Refractory period (milliseconds)
"indicator": "GECI" # one of ["GECI", "GEVI"]
"preset": "jRGECO1a" # preset of "risetime", "decaytime", "dF_F"
# one of ["jGCaMP8f", "jGCaMP8m", "jGCaMP7f", "jRCaMP1a", "jRGECO1a", "Manual"]
# For GECI
"risetime": [25, 25] # Half-rise time (milliseconds)
"decaytime": [350, 350] # Half-decay time from peak (milliseconds)
# For GEVI
"width": [3, 3] # width of a spike (milliseconds)
"subthreshold_std": 0.00 # standard deviation of subthreshold voltage
"subthreshold_filter_std": 100 # standard deviation of subthreshold voltage Gaussian filter standard deviation
# For both GECI/GEVI
"dF_F": [0.1, 0.1] # dF/F0
"photobleaching": 0 # Half-decay time of F0 following exponential function (seconds)
# If 0, no photobleaching.
"baseline": [0.9, 1.1] # baseline (F0)
# each cell sampled from uniform distribution [a, b] as
# F0 depends on protein expression variability.
# F = F0(1+dF/F0) + Normal(0, gaussian_noise)
# Neuronal shape parameters: (underdevelopment)
"shape":
"type": "NLS" # type of neuronal expression.
# one of ["NLS", "cytosolic"(underdevelopment), "soma"(underdevelopment), "membrane"(underdevelopment)]
# "NLS": Nuclear localized expression
# "cytosolic": cytosol expression
# "soma": soma-targeted expression
# "membrane": membrane-targeted expression
"diameter": 8 # diameter of a neuron (micrometer)
"diameter_std": 0.5 # standard deviation of a diameter of a neuron (micrometer)
"diameter_nucleus": 5 # diameter of a nucleus of neurons (micrometer)
"diameter_nucleus_std": 0.20 # standard deviation of a diameter of a nucleus of neurons (micrometer)
"membrane_thickness": 0.2 # thickness of a membrane of neurons (micrometer)
"distance": [5, 10] # min/max distance between neuron and neuron (micrometer)
####################
# NOISE parameters #
####################
# Background spikes (Additive noise)
"background":
"firing_rate": [0.75, 0.75] # mean firing rate (Hz)
# For each neuron, mean firing rate ~ uniform distribution range "low" to "high"
"neuron_ratio": 0.5 # Ratio of neurons oscillate
"peak_to_mean": 0 # (Peak firing rate - mean firing rate) / mean firing rate
# If 0, stationary firing. Cannot be larger than 1.
"oscillation_frequency": 1 # sinusoidal oscillation frequency (Hz)
"coherent": False # If True, oscillation phase is equal to all neurons.
# Otherwise, phase is independently chosen.
# Currently bursting is only available on stationary firing mode.
"burst_lambda": 0 # The number of spikes in each burst follows the Poission process
# The number of spikes = 1 + Poisson(lambda=burst_lambda)
"intra_burst_time": [5, 6] # min/max time between bursting spikes (milliseconds)
# chosen from uniform distribution
# Noise parameters
"noise":
"probabilistic_participation": 1 # probability of a single spike of a motif to appear
# 1: every spike participate.
"temporal_jitter": 0 # standard deviation (milliseconds)
"time_warping": 0 # max additional stretching (percentage)
# 0: No time warping.
# Time warping is only applicable on type 2, 3, and 5 motifs.
####################
# MOTIF parameters #
####################
# type 1 motif: Synchronously firing neurons
"motif_type_1":
"firing_rate": 0.45 # firing rate of each motif
"neurons": 5 # the number of neurons in each motif
"motifs": 1 # the number of motifs
# type 2 motif: Sequentially firing neurons
"motif_type_2":
"firing_rate": 0.1 # firing rate of each motif
"neurons": 5 # the number of neurons in each motif
"motifs": 1 # the number of motifs
"min_lags": 0 # minimum lag between spikes (milliseconds)
"max_lags": 100 # maximum lag between spikes (milliseconds)
# type 3 motif: arbitrary pattern of firing
"motif_type_3":
"firing_rate": 0.1 # firing rate of each motif
"neurons": 5 # the number of neurons in each motif
"motifs": 10 # the number of motifs
"min_lags": 0 # minimum lag between spikes (milliseconds)
"max_lags": 100 # maximum lag between spikes (milliseconds)
"max_spikes": 3 # maximum number of spikes for each neuron to fire in a single motif.
# follows uniform distribution 1 ~ max_spikes.
# type 4 motif: Synchronous increase of firing rate
"motif_type_4":
"firing_rate": 0.3 # firing rate of each motif
"neurons": 5 # the number of neurons in each motif
"motifs": 10 # the number of motifs
"window_size": 0.3 # size of the window (seconds)
"window_rate": 5 # firing rate inside the window (Hz), Poisson.
# type 5 motif: Sequential increase of firing rate
"motif_type_5":
"firing_rate": 0.3 # firing rate of each motif
"neurons": 5 # the number of neurons in each motif
"motifs": 10 # the number of motifs
"window_size": 0.3 # size of the window (seconds)
"window_rate": 5 # firing rate inside the window (Hz), Poisson.
"min_lags": 0 # minimum lag between pattern (milliseconds)
"max_lags": 100 # maximum lag between pattern (milliseconds)