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FLIMJ: an open-source ImageJ toolkit for fluorescence lifetime image data analysis

Dasong Gao, Paul R Barber, View ORCID ProfileJenu V Chacko, View ORCID ProfileMd Abdul Kader Sagar, Curtis T Rueden, Aivar R Grislis, Mark C Hiner, View ORCID ProfileKevin W Eliceiri
doi: https://doi.org/10.1101/2020.08.17.253625
Dasong Gao
1Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
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Paul R Barber
2UCL Cancer Institute, Paul O’Gorman Building, University College London, London, WC1E 6DD, UK
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Jenu V Chacko
1Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
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  • ORCID record for Jenu V Chacko
Md Abdul Kader Sagar
1Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
3Department of Biomedical Engineering, University of Wisconsin, Madison, WI 53706, USA
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Curtis T Rueden
1Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
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Aivar R Grislis
1Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
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Mark C Hiner
1Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
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Kevin W Eliceiri
1Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
3Department of Biomedical Engineering, University of Wisconsin, Madison, WI 53706, USA
4Department of Medical Physics, University of Wisconsin, Madison, WI 53706, USA
5Morgridge Institute for Research, University of Wisconsin, Madison, WI 53706, USA
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  • ORCID record for Kevin W Eliceiri
  • For correspondence: eliceiri@wisc.edu
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Abstract

In the field of fluorescence microscopy, there is continued demand for dynamic technologies that can exploit the complete information from every pixel of an image. One imaging technique with proven ability for yielding additional information from fluorescence imaging is Fluorescence Lifetime Imaging Microscopy (FLIM). FLIM allows for the measurement of how long a fluorophore stays in an excited energy state and is affected by changes in its chemical microenvironment, such as proximity to other fluorophores, pH, and hydrophobic regions. This ability to provide information about the microenvironment has made FLIM a powerful tool for cellular imaging studies ranging from metabolic measurement to measuring distances between proteins. The increased use of FLIM has necessitated the development of computational tools for integrating FLIM analysis with image and data processing. To address this need, we have created FLIMJ, an ImageJ plugin, and toolkit that allows for easy use and development of extensible image analysis workflows with FLIM data. Built on the FLIMLib decay curve fitting library and the ImageJ Ops framework, FLIMJ offers FLIM fitting routines with seamless integration with other ImageJ components, and the ability to be extended to create complex FLIM analysis workflows. Building on ImageJ Ops also enables FLIMJ’s routines to be used with Jupyter notebooks and integrate naturally with science-friendly programming in, e.g., Python and Groovy. We show the extensibility of FLIMJ in two analysis scenarios: lifetime-based image segmentation and image colocalization. We also validate the fitting routines by comparing against industry FLIM analysis standards.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 18, 2020.
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FLIMJ: an open-source ImageJ toolkit for fluorescence lifetime image data analysis
Dasong Gao, Paul R Barber, Jenu V Chacko, Md Abdul Kader Sagar, Curtis T Rueden, Aivar R Grislis, Mark C Hiner, Kevin W Eliceiri
bioRxiv 2020.08.17.253625; doi: https://doi.org/10.1101/2020.08.17.253625
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FLIMJ: an open-source ImageJ toolkit for fluorescence lifetime image data analysis
Dasong Gao, Paul R Barber, Jenu V Chacko, Md Abdul Kader Sagar, Curtis T Rueden, Aivar R Grislis, Mark C Hiner, Kevin W Eliceiri
bioRxiv 2020.08.17.253625; doi: https://doi.org/10.1101/2020.08.17.253625

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