SMS_BP
Single Molecule Simulations -BP
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Documentation for the simulation configuration file of the same name
Simulation Configuration File
Latest version supported: v.0.1
Simulation Configuration File
version: string
version of the simulation configuration file
length_unit: string
length unit of the simulation (e.g. nm, um, mm)
space_unit: string
space unit of the simulation (this is just pixel, should not change)
time_unit: string
time unit of the simulation (e.g. s, ms, us)
intensity_unit: string
intensity unit of the simulation (AUD only supported)
diffusion_unit: string
diffusion unit of the simulation (e.g. um^2/s, mm^2/s)
Cell_Parameters: dict
cell_space: 2D array (units of space_unit)
cell_space[0]: x coordinates of the cell space (min, max)
cell_space[1]: y coordinates of the cell space (min, max)
cell_axial_radius: float (units of space_unit)
The distance from z=0 in either direction that the cell extends
number_of_cells: int
number of cells to simulate (if more than 1 hen all are simulated in one folder defined by the output_path)
Track_Parameters: dict
num_tracks: int
number of tracks to simulate
track_type: string
type of track to simulate ("fbm")
track_length_mean: int (frames)
mean length of the track
track_distribution: string
distribution of the track lengths ("exponential","constant")
diffusion_coefficient: list of floats (units of diffusion_unit)
diffusion coefficient of the track, the length of the list is the unique type of diffusion coefficients
diffusion_track_amount: list of floats
Only viable if allow_transition_probability is False
length is the total number of diffusion coefficients
each element is the probability of the track having the diffusion coefficient at the same index in the diffusion_coefficient list (add up to 1.0)
hurst_expontent: list of floats
hurst exponent of the track, the length of the list is the unique type of hurst exponents
hurst_track_amount: list of floats
Only viable if allow_transition_probability is False
length is the total number of hurst exponents
each element is the probability of the track having the hurst exponent at the same index in the hurst_exponent list (add up to 1.0)
allow_transition_probability: bool
whether to allow transition probabilities between different diffusion coefficients and hurst exponents within a track
if false, the track will have a single diffusion coefficient and hurst exponent
transition_matrix_time_step: int
time step at which the diffusion and hurst exponent transition matrices are supplied in the following parameters
the units are in time_unit (so 100 ms would be 100)
diffusion_transition_matrix: 2D array (discrete state probabilitiy at the transition_matrix_time_step = dt)
transition matrix between different diffusion coefficients
rows are the current diffusion coefficient
columns are the next diffusion coefficient
rows must sum to 1.0
hurst_transition_matrix: 2D array (discrete state probabilitiy at the transition_matrix_time_step = dt)
transition matrix between different hurst exponents
rows are the current hurst exponent
columns are the next hurst exponent
rows must sum to 1.0
state_probability_diffusion: 1D array (probability)
probability of a track being in a certain diffusion coefficient state
length is the number of unique diffusion coefficients
state_probability_hurst: 1D array (probability)
probability of a track being in a certain hurst exponent state
length is the number of unique hurst exponents
Global_Parameters: dict
field_of_view_dim: 1D array (units of space_unit)
field of view dimensions (x,y (pixels))
frame_count: int
number of frames to simulate
exposure_time: float or int (units of time_unit)
exposure time of the camera
interval_time: float or int (units of time_unit)
time between frames that the camera is on
oversample_motion_time: float or int (units of time_unit)
oversampling the motion for motion blur
if oversample_motion_time == frame_time == exposure_time, then there is no motion blur
cannot be greater than frame_time or exposure_time
pixel_size: float (units of length_unit)
size of the pixel
axial_detection_range: float (units of length_unit)
from z=0, the distance in either direction that the camera can detect a single molecule excitation
base_noise: float (units of intensity_unit)
base noise of the camera (offset)
point_intensity: float (units of intensity_unit)
intensity of a single molecule excitation
psf_sigma: float (units of length_unit)
size of the psf (assumed to be gaussian)
axial_function: string ("exponential","ones"(no effect))
function used to determine how the intensity of the single molecule changes with z
Condenstate_Parameters: dict
initial_centers: 2D array (units of space_unit)
initial centers of the condensates
[x,y,z] coordinates per row
number of rows is the number of condensates
initial_scale: 1D (units of space_unit)
initial radius of the condensates
number of elements is the number of condensates
must be the same length as initial_centers
diffusion_coefficient: 1D array (units of diffusion_unit)
diffusion coefficient of the condensates
number of elements is the number of condensates
must be the same length as initial_centers
hurst_exponent: 1D array
hurst exponent of the condensates
number of elements is the number of condensates
must be the same length as initial_centers
density_dif: float
density difference between the condensates and the rest of the cell
Output_Parameters: dict
output_path: string
path to save the output, directory
output_name: string
name of the output file *subsegment_type: string
function used to do projections ("mean","max","sum")
subsegment_number: int
number of subsegments to divide the cell frames into
if total movie is 500 frames and this is 5 then there will be 100 frames per subsegment and 5 subsegments in total
Make sure that the total number of frames is divisible by the number of subsegments (modulus is 0)
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