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Tan KKD, Tsuchida MA, Chacko JV, Gahm NA, Eliceiri KW. Real-time open-source FLIM analysis. FRONTIERS IN BIOINFORMATICS 2023; 3:1286983. [PMID: 38098814 PMCID: PMC10720713 DOI: 10.3389/fbinf.2023.1286983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/08/2023] [Indexed: 12/17/2023] Open
Abstract
Fluorescence lifetime imaging microscopy (FLIM) provides valuable quantitative insights into fluorophores' chemical microenvironment. Due to long computation times and the lack of accessible, open-source real-time analysis toolkits, traditional analysis of FLIM data, particularly with the widely used time-correlated single-photon counting (TCSPC) approach, typically occurs after acquisition. As a result, uncertainties about the quality of FLIM data persist even after collection, frequently necessitating the extension of imaging sessions. Unfortunately, prolonged sessions not only risk missing important biological events but also cause photobleaching and photodamage. We present the first open-source program designed for real-time FLIM analysis during specimen scanning to address these challenges. Our approach combines acquisition with real-time computational and visualization capabilities, allowing us to assess FLIM data quality on the fly. Our open-source real-time FLIM viewer, integrated as a Napari plugin, displays phasor analysis and rapid lifetime determination (RLD) results computed from real-time data transmitted by acquisition software such as the open-source Micro-Manager-based OpenScan package. Our method facilitates early identification of FLIM signatures and data quality assessment by providing preliminary analysis during acquisition. This not only speeds up the imaging process, but it is especially useful when imaging sensitive live biological samples.
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Affiliation(s)
- Kevin K. D. Tan
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI, United States
| | - Mark A. Tsuchida
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI, United States
| | - Jenu V. Chacko
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI, United States
| | - Niklas A. Gahm
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI, United States
- Morgridge Institute for Research, Madison, WI, United States
| | - Kevin W. Eliceiri
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, United States
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI, United States
- Morgridge Institute for Research, Madison, WI, United States
- Department of Medical Physics, University of Wisconsin, Madison, WI, United States
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Bitton A, Sambrano J, Valentino S, Houston JP. A Review of New High-Throughput Methods Designed for Fluorescence Lifetime Sensing From Cells and Tissues. FRONTIERS IN PHYSICS 2021; 9:648553. [PMID: 34007839 PMCID: PMC8127321 DOI: 10.3389/fphy.2021.648553] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Though much of the interest in fluorescence in the past has been on measuring spectral qualities such as wavelength and intensity, there are two other highly useful intrinsic properties of fluorescence: lifetime (or decay) and anisotropy (or polarization). Each has its own set of unique advantages, limitations, and challenges in detection when it comes to use in biological studies. This review will focus on the property of fluorescence lifetime, providing a brief background on instrumentation and theory, and examine the recent advancements and applications of measuring lifetime in the fields of high-throughput fluorescence lifetime imaging microscopy (HT-FLIM) and time-resolved flow cytometry (TRFC). In addition, the crossover of these two methods and their outlooks will be discussed.
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Affiliation(s)
- Aric Bitton
- Department of Chemical and Materials Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Jesus Sambrano
- Department of Chemical and Materials Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Samantha Valentino
- Department of Chemical and Materials Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Jessica P. Houston
- Department of Chemical and Materials Engineering, New Mexico State University, Las Cruces, NM, United States
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Barkauskas DS, Medley G, Liang X, Mohammed YH, Thorling CA, Wang H, Roberts MS. Using in vivo multiphoton fluorescence lifetime imaging to unravel disease-specific changes in the liver redox state. Methods Appl Fluoresc 2020; 8:034003. [PMID: 32422610 DOI: 10.1088/2050-6120/ab93de] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multiphoton fluorescence lifetime microscopy has revolutionized studies of pathophysiological and xenobiotic dynamics, enabling the spatial and temporal quantification of these processes in intact organs in vivo. We have previously used multiphoton fluorescence lifetime microscopy to characterise the morphology and amplitude weighted mean fluorescence lifetime of the endogenous fluorescent metabolic cofactor nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) of mouse livers in vivo following induction of various disease states. Here, we extend the characterisation of liver disease models by using nonlinear regression to estimate the unbound, bound fluorescence lifetimes for NAD(P)H, flavin adenine dinucleotide (FAD), along with metabolic ratios and examine the impact of using multiple segmentation methods. We found that NAD(P)H amplitude ratio, and fluorescence lifetime redox ratio can be used as discriminators of diseased liver from normal liver. The redox ratio provided a sensitive measure of the changes in hepatic fibrosis and biliary fibrosis. Hepatocellular carcinoma was associated with an increase in spatial heterogeneity and redox ratio coupled with a decrease in mean fluorescence lifetime. We conclude that multiphoton fluorescence lifetime microscopy parameters and metabolic ratios provided insights into the in vivo redox state of diseased compared to normal liver that were not apparent from a global, mean fluorescence lifetime measurement alone.
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Affiliation(s)
- Deborah S Barkauskas
- Therapeutics Research Group, University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
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