ratioExpPhysio {CalciOMatic}R Documentation

Gathers the Results of a Ratiometric Experiment in an Object of Class "fluo_rawdata"

Description

The function ratioExpPhysio gathers the results of a single ratiometric experiment including 1 or more fluorescence transients in a data frame of class "fluo_rawdata", usable by the following functions: ratioFitFromDf, directFit and plot.fluo_rawdata

Usage

ratioExpPhysio(dataset = "inVitro", expe = 1, stim = 1, idxOn = 10,
               R_min = 0.136, R_max = 2.701, K_eff = 3.637, K_d = 0.583,
               G = 0.146, s_ro = 16.4, alphamethod = TRUE)

Arguments

dataset a character string. The name of the variable containing results of ratiometric experiments. The minimal structure of this variable is detailed in inVitro
expe the number of the experiment to consider (field "Exp.." of the dataset)
stim a vector of integers specifying the number of the stimulations to consider (field "stim.")
idxOn the index of the time at which the stimulation is applied
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
G the gain of the CCD camera
s_ro the standard deviation of the read-out process of the camera
alphamethod a logical value. If set to TRUE, the fluorescence measurements at 360 nm (contained in the dataset) are used to estimate the isocoefficient alpha

Details

Details about the estimation of the isocoefficient alpha with the fluorescence measurements at 340, 380 and 360 nm are given in Joucla et al. (2009, J Neurophysiol) (see Methods and Appendix C)

The variable entitled "dataset", which contains all experiment informations, should be a list with fields named "Exp01", "Exp02", etc. Each of this field should be a list with (at least) the following fields. The information contained in these fields are retrieved and put at the right place in the output data frame:
stim1 (eventually stim2, stim3, etc.)
adu340Background a vector of background fluorescence recorded at 340 nm
adu380Background a vector of background fluorescence recorded at 380 nm
P the number of pixels used for the data binning of the raw image,
for fluorescence transient
PBackground the number of pixels used for the data binning of the raw image,
for background fluorescence
furaPipette the total concentration of the dye in the pipette (in muM)
which is assumed to be the same in the cell, at steady-state
exposureTime340 the exposure time at 340 nm (in s)
exposureTime380 the exposure time at 380 nm (in s)

Each field of "stim1" should be a list with at least the following fields:
time the times at which the fluorescence transient was acquired
adu340 the fluorescence transient obtained at 340 nm
adu380 the fluorescence transient obtained at 380 nm

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 times 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 field P of the input data set
P_B a copy of arg PBackground of the input data set
B_T the total Fura concentration in the cell (in muM)
nb_B the number of background measurements performed at each wavelength, before loading the dye into the cell
alpha an estimation of the isocoefficient (only if alphamethod is set to TRUE)
G a copy of arg G
s_ro a copy of arg s_ro

Author(s)

Sebastien Joucla sebastien.joucla@parisdescartes.fr

See Also

ratioExpSimul

Examples

## Load the data from cockroach olfactory interneurons
data(inVitro)

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

## Create the data frame containing the physiological data
## (experiment #2, stimulation #2)
## G and s_ro are the respectively the gain of the CCD camera
## and the standard deviation of its read-out process
physioData <- ratioExpPhysio(dataset="inVitro",
                             expe=2, stim=2,
                             idxOn=10,
                             R_min=R_min, R_max=R_max,
                             K_eff=K_eff, K_d=K_d,
                             G=0.146, s_ro=16.4,
                             alphamethod=TRUE)

## Plot the raw data
plot(physioData, numTransient=2)

[Package CalciOMatic version 1.1-3 Index]