ratioExpSimul {CalciOMatic}R Documentation

Simulate Ratiometric Experiment

Description

The function ratioExpSimul simulates the results of one ratiometric experiment, i.e, the photon counts obtained at both wavelengths (340 and 380 nm), knowing the time course of the intracellular calcium concentration. The photon counts are described as the realization of a Poissonian process.

Usage

ratioExpSimul(nb_B = 5, Ca,
              R_min = 0.136, R_max = 2.701, K_eff = 3.637, K_d = 0.583,
              B_T = 100, phi = 1.25, S_B_340 = 10, S_B_380 = 10,
              T_340 = 0.015, T_380 = 0.006, P = 400, P_B = 400,
              ntransients = 1, G = 1, s_ro = 0, noise = TRUE)

Arguments

nb_B the number of background measurements to simulate before the fluorescence transients
Ca the ideal calcium transient from which fluorescence signales arise
R_min the minimum fluorescence ratio between the measurements at 340 and 380 nm. This parameter is obtained from calibration experiments
R_max the maximum fluorescence ratio between the measurements at 340 and 380 nm. This parameter is obtained from calibration experiments
K_eff the effective dissociation constant of the dye in the cell (in muM). This parameter is obtained from calibration experiments
K_d the dissociation constant of the dye in the cell (in muM). This parameter is obtained from calibration experiments
B_T the total concentration of the dye in the cell (in muM)
phi the scaling experiment-specific parameters
S_B_340 the background fluorescence at 340 nm
S_B_380 the background fluorescence at 380 nm
T_340 the exposure time at 340 nm
T_380 the exposure time at 380 nm
P the number of pixels of the ROI
P_B the number of pixels of the background region
ntransients a vector of integers (above or equal to 1) specifying the indices of the transients to simulate
G the gain of the CCD camera
s_ro the standard deviation of the read-out process of the camera
noise a logical. see details below

Details

The way fluorescence values arise from intracellular calcium concentration values is described in the fluo function. Recording fluorescence with a CCD camera noises the photon counts, which can be described as the realization of a Poissonian process, the parameter of which is the fluorescence value itself. Ratiometric experiments are simulated thus simulated by drawing Poissonian samples from ideal fluorescence transients. These noisy data are then multiplied bu the gain G of the CCD camera, and the standard deviation of the read-out noise (s_ro) is finally added. In case noise is set to FALSE, fluorescence data arising from the fluorescence model are only digitized (rounded towards the nearest integer), but not drawn from a Poisson distribution.

Value

An object of class "fluo_rawdata", which is a data frame with four columns:
adu the photon counts (or Analog-to-Digital Units) at both wavelengths,
including background fluorescence
Time the times at which each value in adu was recorded.
For the background fluorescence, Time is set to NA
lambda the wavelength at which each value in adu was recorded (a factor)
transient the number of the fluorescence transient in the input data (can be 1, 2 or 3
for transient signals, and 0 for background measurements)
Data appear in this order : (1) the background fluorescence at 340 nm, (2) the fluorescence transient(s) at 340 nm, (3) the background fluorescence at 380 nm, (4) the fluorescence transient(s) at 380 nm. The object has also the following attributes:

tOn the time at which the stimulation is applied (in s)
T_stim a vector containing the exposure time at 340 nm and 380 nm
R_min a copy of arg R_min
R_max a copy of arg R_max
K_eff a copy of arg K_eff
K_d a copy of arg K_d
P a copy of arg P
P_B a copy of arg P_B
B_T a copy of arg B_T
nb_B a copy of arg nb_B
G a copy of arg G
s_ro a copy of arg s_ro

Author(s)

Sebastien Joucla sebastien.joucla@parisdescartes.fr

See Also

ratioExpPhysio

Examples

## Parameters of the monoexponential calcium transient
tOn  <- 1
Time <- seq(0,12,length.out=160)
Ca0  <- 0.10
dCa  <- 0.25
tau  <- 1.5

## Calibrated parameters
R_min <- list(value=0.136, mean=0.136, se=0.00363, USE_se=FALSE)
R_max <- list(value=2.701, mean=2.701, se=0.151,   USE_se=FALSE)
K_eff <- list(value=3.637, mean=3.637, se=0.729,   USE_se=FALSE)
K_d   <- list(value=0.583, mean=0.583, se=0.123,   USE_se=FALSE)

## Experiment-specific parameters
nb_B    <- 1
B_T     <- 100.0
T_340   <- 0.015
T_380   <- 0.006
P       <- 200
P_B     <- 200
phi     <- 2
S_B_340 <- 30
S_B_380 <- 80

## Create a monoexponential calcium decay
Ca <- caMonoExp(t = Time, tOn = tOn,
                Ca0 = Ca0, dCa = dCa, tau = tau)

## Simulate the corresponding ratiometric experiment
simulData <- ratioExpSimul(nb_B    = nb_B,
                           Ca      = Ca,
                           R_min   = R_min,
                           R_max   = R_max,
                           K_eff   = K_eff,
                           K_d     = K_d,
                           B_T     = B_T,
                           phi     = phi,
                           S_B_340 = S_B_340,
                           S_B_380 = S_B_380,
                           T_340   = T_340,
                           T_380   = T_380,
                           P       = P,
                           P_B     = P_B,
                           ntransients = 1,
                           G       = 1,
                           s_ro    = 0)

## Plot the raw data
plot(simulData, numTransient=1)

[Package CalciOMatic version 1.1-3 Index]