Published by the Foundation for Open Access Statistics Editors-in-chief: Bettina Grün, Torsten Hothorn, Rebecca Killick, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Authors: Sergey Laptenok, Katharine M. Mullen, Jan Willem Borst, Ivo H. M. van Stokkum, Vladimir V. Apanasovich, Antonie J. W. G. Visser
Title: Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP
Abstract: Fluorescence Lifetime Imaging Microscopy (FLIM) allows fluorescence lifetime images of biological objects to be collected at 250 nm spatial resolution and at (sub-)nanosecond temporal resolution. Often ncomp kinetic processes underlie the observed fluorescence at all locations, but the intensity of the fluorescence associated with each process varies per-location, i.e., per-pixel imaged. Then the statistical challenge is global analysis of the image: use of the fluorescence decay in time at all locations to estimate the ncomp lifetimes associated with the kinetic processes, as well as the amplitude of each kinetic process at each location. Given that typical FLIM images represent on the order of 102 timepoints and 103 locations, meeting this challenge is computationally intensive. Here the utility of the TIMP package for R to solve parameter estimation problems arising in FLIM image analysis is demonstrated. Case studies on simulated and real data evidence the applicability of the partitioned variable projection algorithm implemented in TIMP to the problem domain, and showcase options included in the package for the visual validation of models for FLIM data.

Page views:: 9759. Submitted: 2006-12-11. Published: 2007-01-10.
Paper: Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP     Download PDF (Downloads: 9863)
Supplements: Folder of Data sets and R scripts Download (Downloads: 2617; 411KB)
TIMP_1.0.tar.gz: R source package Download (Downloads: 2417; 814KB) R Windows Binary Download (Downloads: 2365; 126KB)

DOI: 10.18637/jss.v018.i08

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Paper: Creative Commons Attribution 3.0 Unported License
Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.