IDEAS home Printed from https://ideas.repec.org/a/jss/jstsof/v018i08.html
   My bibliography  Save this article

Fluorescence Lifetime Imaging Microscopy (FLIM) Data Analysis with TIMP

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.jstatsoft.org/index.php/jss/article/view/v018i08/v18i08.pdf
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v018i08/CODE.zip
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v018i08/TIMP_1.0.tar.gz
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v018i08/TIMP_1.0.zip
    Download Restriction: no
    File URL: https://libkey.io/http://hdl.handle.net/10.18637/jss.v018.i08?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    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).
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    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).

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Chong Wang & Bo Wu & Yang Li & Shen Zhou & Conghui Wu & Tianyang Dong & Ying Jiang & Zihui Hua & Yupeng Song & Wei Wen & Jianxin Tian & Yongqiang Chai & Rui Wen & Chunru Wang, 2024. "Aggregation promotes charge separation in fullerene-indacenodithiophene dyad," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Wei Wen & Guocai Liu & Xiaofang Wei & Haojie Huang & Chong Wang & Danlei Zhu & Jianzhe Sun & Huijuan Yan & Xin Huang & Wenkang Shi & Xiaojuan Dai & Jichen Dong & Lang Jiang & Yunlong Guo & Hanlin Wang, 2024. "Biomimetic nanocluster photoreceptors for adaptative circular polarization vision," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    3. Adelina Bärligea & Philipp Hochstaffl & Franz Schreier, 2023. "A Generalized Variable Projection Algorithm for Least Squares Problems in Atmospheric Remote Sensing," Mathematics, MDPI, vol. 11(13), pages 1-20, June.
    4. Dianne O’Leary & Bert Rust, 2013. "Variable projection for nonlinear least squares problems," Computational Optimization and Applications, Springer, vol. 54(3), pages 579-593, April.
    5. repec:jss:jstsof:18:i08 is not listed on IDEAS

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:jss:jstsof:v:018:i08. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Christopher F. Baum (email available below). General contact details of provider: http://www.jstatsoft.org/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.