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