CalciOMatic-package {CalciOMatic}R Documentation

Automatic Calcium Imaging Analysis

Description

Simulate and analyse calcium imaging data obtained with ratiometric dyes. The package provides tools to fit parametric models of calcium dynamics on experimental data. Two methods are available: the classical 'ratiometric' method and a new 'direct' method, which does not imply any data ratioing and fits directly the fluorescence transients recorded at two excitation wavelengths. The latter method allows for the construction of meaningful confidence intervals on the calcium dynamics parameters.

Details

Package: CalciOMatic
Type: Package
Version: 1.1-3
Date: 2009-10-06
License: GPL (>= 2)
Depends: cobs

Author(s)

Sebastien Joucla, Christophe Pouzat

Maintainer: Sebastien Joucla <sebastien.joucla@parisdescartes.fr>

References

Joucla S, Pippow A, Kloppenburg P and Pouzat C (2009) Quantitative estimation of calcium dynamics from ratiometric measurements: A direct, non-ratioing, approach. J Neurophyiol, in revision

Examples

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

## Define the calibrated parameters of the calcium indicator (Fura-2)
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)

## Characteristics of the CCD camera, obtained from 'calibration' experiments
G    <- 0.146
s_ro <- 16.4

## Create the data.frame containing the physiological data:
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=G, s_ro=s_ro,
                             alphamethod=TRUE)

## Fit the physiological data with the direct method:
physioDirectFit <- directFit(physioData,
                             transients=2,
                             SQRT=TRUE,
                             type="mono",
                             AfterPeak=14)

## Plot the raw and fitted data, as well as plots of goodness of fit
plot(physioDirectFit, numTransient=2, items=1:6)

[Package CalciOMatic version 1.1-3 Index]