title: Estimating background-subtracted fluorescence transients in calcium imaging experiments: a quantitative approach.
abstract: Calcium imaging has become a routine technique in neuroscience for subcellular to network level investigations. The fast progresses in the development of new indicators and imaging techniques call for dedicated reliable analysis methods. In particular, efficient and quantitative background fluorescence subtraction routines would be beneficial to most of the calcium imaging research field. A background-subtracted fluorescence transients estimation method that does not require any independent background measurement is therefore developed. This method is based on a fluorescence model fitted to single-trial data using a classical nonlinear regression approach. The model includes an appropriate probabilistic description of the acquisition system's noise leading to accurate confidence intervals on all quantities of interest (background fluorescence, normalized background-subtracted fluorescence time course) when background fluorescence is homogeneous. An automatic procedure detecting background inhomogeneities inside the region of interest is also developed and is shown to be efficient on simulated data. The implementation and performances of the proposed method on experimental recordings from the mouse hypothalamus are presented in details. This method, which applies to both single-cell and bulk-stained tissues recordings, should help improving the statistical comparison of fluorescence calcium signals between experiments and studies.
authors.affiliation: Cerebral Physiology Laboratory, Université Paris-Descartes, CNRS, UMR 8118, 45 rue des Saints-Pères, 75006 Paris, France. sebastien.joucla@u-bordeaux1.fr
authors.forename: Sébastien
authors.initials: S
authors.lastname: Joucla
authors.forename: Romain
authors.initials: R
authors.lastname: Franconville
authors.forename: Andreas
authors.initials: A
authors.lastname: Pippow
authors.forename: Peter
authors.initials: P
authors.lastname: Kloppenburg
authors.forename: Christophe
authors.initials: C
authors.lastname: Pouzat
mesh_terms: D000818:Animals; D002118:Calcium / Q000378:metabolism*; D020013:Calcium Signaling / Q000502:physiology; D049452:Green Fluorescent Proteins / Q000378:metabolism*; D007031:Hypothalamus / Q000166:cytology / Q000378:metabolism*; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D023421:Models, Animal; D008954:Models, Biological; D009474:Neurons / Q000166:cytology / Q000378:metabolism*; D061848:Optical Imaging / Q000379:methods*; D011333:Pro-Opiomelanocortin / Q000378:metabolism; D012044:Regression Analysis; D015203:Reproducibility of Results; D013997:Time Factors
chemical_list: D049452:Green Fluorescent Proteins; D011333:Pro-Opiomelanocortin; D002118:Calcium
keywords: Confidence intervals; Fluorescence model; Goodness-of-fit tests; Maximum likelihood estimate; Mouse hypothalamus neurons; Quantitative imaging