ratioExpSimul {CalciOMatic} | R Documentation |
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.
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)
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 |
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.
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) |
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 |
Sebastien Joucla sebastien.joucla@parisdescartes.fr
## 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)