mkFluo4DirectFit {CalciOMatic}R Documentation

Define Predicted Fluorescence Signals

Description

The function mkFluo4DirectFit defines a single signal made of four fluorescence signals (the background and fluorescence transients at both wavelengths), for use with within the mkFunction4DirectFit function

Usage

mkFluo4DirectFit(Ca, phi, S_B_340, S_B_380, nb_B,
                 R_min, R_max, K_eff, K_d, B_T,
                 T_340, T_380, P, P_B, SQRT = TRUE)

Arguments

Ca the time course of the intracellular calcium concentration
phi the scaling experiment-specific parameter
S_B_340 the background fluorescence at 340 nm
S_B_380 the background fluorescence at 380 nm
nb_B the number of background measurements
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 inside the cell (in muM)
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
SQRT a logical value. Set to TRUE to apply the square root transformation to the fluorescence signals

Value

a vector containing, in this order: the background fluorescence (in count) at 340 nm, the fluorescence transient at 340 nm, the background fluorescence at 380 nm and the fluorescence transient at 380 nm. If the SQRT argument is set to TRUE, the square root of the whole signal is returned

Author(s)

Sebastien Joucla sebastien.joucla@parisdescartes.fr

See Also

mkFunction4DirectFit, directFit

Examples

## Parameters of the biexponential calcium transient
tOn <- 1
Time <- seq(0,12,length.out=160)
Ca0 <- 0.10
dCa <- 0.25
tau <- 1.5
mu <- 0
dtau <- 10

## Calibration parameters
R_min <- 0.136
R_max <- 2.701
K_eff <- 3.637
K_d   <- 0.583

## 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 biexponential calcium decay
Ca_Bi <- caBiExp(t=Time,
                 tOn=tOn,
                 Ca0=Ca0,
                 dCa=dCa,
                 tau=tau,
                 fact=1/(1+exp(-mu)),
                 dtau=dtau)

## Define the whole original fluorescence vector
Fluo_bi <- mkFluo4DirectFit(Ca = Ca_Bi, phi,
                            S_B_340, S_B_380, nb_B,
                            R_min, R_max, K_eff, K_d,
                            B_T, T_340, T_380, P, P_B,
                            SQRT = TRUE)

[Package CalciOMatic version 1.1-3 Index]