mkFluo4DirectFit {CalciOMatic} | R Documentation |
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
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)
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 |
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
Sebastien Joucla sebastien.joucla@parisdescartes.fr
mkFunction4DirectFit
,
directFit
## 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)