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Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP

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  • Laptenok, Sergey
  • Mullen, Katharine M.
  • Borst, Jan Willem
  • van Stokkum, Ivo H. M.
  • Apanasovich, Vladimir V.
  • Visser, Antonie J. W. G.

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.

Suggested Citation

  • Laptenok, Sergey & Mullen, Katharine M. & Borst, Jan Willem & van Stokkum, Ivo H. M. & Apanasovich, Vladimir V. & Visser, Antonie J. W. G., 2007. "Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 18(i08).
    • Handle: RePEc:jss:jstsof:v:018:i08
    DOI: http://hdl.handle.net/10.18637/jss.v018.i08
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    1. Mullen, Katharine M. & van Stokkum, Ivo H. M., 2007. "TIMP: An R Package for Modeling Multi-way Spectroscopic Measurements," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 18(i03).
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    Cited by:

    1. Matthias Klemm & Dietrich Schweitzer & Sven Peters & Lydia Sauer & Martin Hammer & Jens Haueisen, 2015. "FLIMX: A Software Package to Determine and Analyze the Fluorescence Lifetime in Time-Resolved Fluorescence Data from the Human Eye," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-28, July.
    2. repec:jss:jstsof:18:i03 is not listed on IDEAS
    3. Mullen, Katharine M. & van Stokkum, Ivo H. M., 2007. "TIMP: An R Package for Modeling Multi-way Spectroscopic Measurements," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 18(i03).
    4. Snellenburg, Joris J. & Laptenok, Sergey & Seger, Ralf & Mullen, Katharine M. & van Stokkum, Ivo H. M., 2012. "Glotaran: A Java-Based Graphical User Interface for the R Package TIMP," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 49(i03).

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