Nonparametric empirical Bayesian framework for fluorescence-lifetime imaging microscopy
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a powerful imaging tool used to study the molecular environment of flurophores. In time domain FLIM, extracting lifetime from fluorophores signals entails fitting data to a decaying exponential distribution function. However, most existing techniques for this purpose need large amounts of photons at each pixel and a long computation time, thus making it difficult to obtain reliable inference in applications requiring either short acquisition or minimal computation time. In this work, we introduce a new nonparametric empirical Bayesian framework for FLIM data analysis (NEB-FLIM), leading to both improved pixel-wise lifetime estimation and a more robust and computationally efficient integral property inference. This framework is developed based on a newly proposed hierarchical statistical model for FLIM data and adopts a novel nonparametric maximum likelihood estimator to estimate the prior distribution. To demonstrate the merit of the proposed framework, we applied it on both simulated and real biological datasets and compared it with previous classical methods on these datasets.
- Authors:
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1569103
- Alternate Identifier(s):
- OSTI ID: 1803493
- Grant/Contract Number:
- SC0019013
- Resource Type:
- Published Article
- Journal Name:
- Biomedical Optics Express
- Additional Journal Information:
- Journal Name: Biomedical Optics Express Journal Volume: 10 Journal Issue: 11; Journal ID: ISSN 2156-7085
- Publisher:
- Optical Society of America
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Biochemistry & Molecular Biology; Optics; Radiology, Nuclear Medicine & Medical Imaging
Citation Formats
Wang, Shulei, Chacko, Jenu V., Sagar, Abdul K., Eliceiri, Kevin W., and Yuan, Ming. Nonparametric empirical Bayesian framework for fluorescence-lifetime imaging microscopy. United States: N. p., 2019.
Web. doi:10.1364/BOE.10.005497.
Wang, Shulei, Chacko, Jenu V., Sagar, Abdul K., Eliceiri, Kevin W., & Yuan, Ming. Nonparametric empirical Bayesian framework for fluorescence-lifetime imaging microscopy. United States. https://doi.org/10.1364/BOE.10.005497
Wang, Shulei, Chacko, Jenu V., Sagar, Abdul K., Eliceiri, Kevin W., and Yuan, Ming. Thu .
"Nonparametric empirical Bayesian framework for fluorescence-lifetime imaging microscopy". United States. https://doi.org/10.1364/BOE.10.005497.
@article{osti_1569103,
title = {Nonparametric empirical Bayesian framework for fluorescence-lifetime imaging microscopy},
author = {Wang, Shulei and Chacko, Jenu V. and Sagar, Abdul K. and Eliceiri, Kevin W. and Yuan, Ming},
abstractNote = {Fluorescence lifetime imaging microscopy (FLIM) is a powerful imaging tool used to study the molecular environment of flurophores. In time domain FLIM, extracting lifetime from fluorophores signals entails fitting data to a decaying exponential distribution function. However, most existing techniques for this purpose need large amounts of photons at each pixel and a long computation time, thus making it difficult to obtain reliable inference in applications requiring either short acquisition or minimal computation time. In this work, we introduce a new nonparametric empirical Bayesian framework for FLIM data analysis (NEB-FLIM), leading to both improved pixel-wise lifetime estimation and a more robust and computationally efficient integral property inference. This framework is developed based on a newly proposed hierarchical statistical model for FLIM data and adopts a novel nonparametric maximum likelihood estimator to estimate the prior distribution. To demonstrate the merit of the proposed framework, we applied it on both simulated and real biological datasets and compared it with previous classical methods on these datasets.},
doi = {10.1364/BOE.10.005497},
journal = {Biomedical Optics Express},
number = 11,
volume = 10,
place = {United States},
year = {2019},
month = {10}
}
https://doi.org/10.1364/BOE.10.005497
Web of Science
Works referenced in this record:
Convex Optimization, Shape Constraints, Compound Decisions, and Empirical Bayes Rules
journal, April 2014
- Koenker, Roger; Mizera, Ivan
- Journal of the American Statistical Association, Vol. 109, Issue 506
Global and pixel kinetic data analysis for FRET detection by multi-photon time-domain FLIM
conference, March 2005
- Barber, Paul R.; Ameer-Beg, Simon M.; Gilbey, Julian D.
- Biomedical Optics 2005, SPIE Proceedings
Compound decision theory and empirical Bayes methods: invited paper
journal, April 2003
- Zhang, Cun-Hui
- The Annals of Statistics, Vol. 31, Issue 2
Metabolic Mapping of MCF10A Human Breast Cells via Multiphoton Fluorescence Lifetime Imaging of the Coenzyme NADH
journal, October 2005
- Bird, Damian K.; Yan, Long; Vrotsos, Kristin M.
- Cancer Research, Vol. 65, Issue 19
Evaluation of global analysis algorithms for single frequency fluorescence lifetime imaging microscopy data
journal, January 2003
- Verveer, P. J.; Bastiaens, P. I. H.
- Journal of Microscopy, Vol. 209, Issue 1
Automated High-Throughput Fluorescence Lifetime Imaging Microscopy to Detect Protein–Protein Interactions
journal, April 2016
- Guzmán, Camilo; Oetken-Lindholm, Christina; Abankwa, Daniel
- Journal of Laboratory Automation, Vol. 21, Issue 2
The Geometry of Mixture Likelihoods: A General Theory
journal, March 1983
- Lindsay, Bruce G.
- The Annals of Statistics, Vol. 11, Issue 1
Bayesian analysis of fluorescence lifetime imaging data
conference, February 2011
- Rowley, Mark I.; Barber, Paul R.; Coolen, Anthony C. C.
- SPIE BiOS, SPIE Proceedings
Developing and Testing a Bayesian Analysis of Fluorescence Lifetime Measurements
journal, January 2017
- Kaye, Bryan; Foster, Peter J.; Yoo, Tae Yeon
- PLOS ONE, Vol. 12, Issue 1
The Bernstein-Von-Mises theorem under misspecification
journal, January 2012
- Kleijn, B. J. K.; van der Vaart, A. W.
- Electronic Journal of Statistics, Vol. 6, Issue 0
Photon Counting Data Analysis: Application of the Maximum Likelihood and Related Methods for the Determination of Lifetimes in Mixtures of Rose Bengal and Rhodamine B
journal, December 2016
- Santra, Kalyan; Smith, Emily A.; Petrich, Jacob W.
- The Journal of Physical Chemistry A, Vol. 121, Issue 1
Consistency of the Maximum Likelihood Estimator in the Presence of Infinitely Many Incidental Parameters
journal, December 1956
- Kiefer, J.; Wolfowitz, J.
- The Annals of Mathematical Statistics, Vol. 27, Issue 4
What Is the Best Method to Fit Time-Resolved Data? A Comparison of the Residual Minimization and the Maximum Likelihood Techniques As Applied to Experimental Time-Correlated, Single-Photon Counting Data
journal, February 2016
- Santra, Kalyan; Zhan, Jinchun; Song, Xueyu
- The Journal of Physical Chemistry B, Vol. 120, Issue 9
In vivo multiphoton fluorescence lifetime imaging of protein-bound and free nicotinamide adenine dinucleotide in normal and precancerous epithelia
journal, January 2007
- Skala, Melissa C.; Riching, Kristin M.; Bird, Damian K.
- Journal of Biomedical Optics, Vol. 12, Issue 2
An Experimental Comparison of the Maximum Likelihood Estimation and Nonlinear Least-Squares Fluorescence Lifetime Analysis of Single Molecules
journal, May 2001
- Maus, Michael; Cotlet, Mircea; Hofkens, Johan
- Analytical Chemistry, Vol. 73, Issue 9
Simple and Globally Convergent Methods for Accelerating the Convergence of Any EM Algorithm
journal, June 2008
- Varadhan, Ravi; Roland, Christophe
- Scandinavian Journal of Statistics, Vol. 35, Issue 2
Optical Metabolic Imaging Identifies Glycolytic Levels, Subtypes, and Early-Treatment Response in Breast Cancer
journal, October 2013
- Walsh, A. J.; Cook, R. S.; Manning, H. C.
- Cancer Research, Vol. 73, Issue 20
A Bayesian method for single molecule, fluorescence burst analysis
journal, January 2010
- Barber, P. R.; Ameer-Beg, S. M.; Pathmananthan, S.
- Biomedical Optics Express, Vol. 1, Issue 4
How many photons are necessary for fluorescence-lifetime measurements?
journal, November 1992
- Köllner, Malte; Wolfrum, Jürgen
- Chemical Physics Letters, Vol. 200, Issue 1-2
Autofluorescence lifetime imaging of cellular metabolism: Sensitivity toward cell density, pH, intracellular, and intercellular heterogeneity: FLIM sensitivity towards pH, heterogeneity and confluency
journal, October 2018
- Chacko, Jenu V.; Eliceiri, Kevin W.
- Cytometry Part A, Vol. 95, Issue 1
Rapid Global Fitting of Large Fluorescence Lifetime Imaging Microscopy Datasets
journal, August 2013
- Warren, Sean C.; Margineanu, Anca; Alibhai, Dominic
- PLoS ONE, Vol. 8, Issue 8
General maximum likelihood empirical Bayes estimation of normal means
journal, August 2009
- Jiang, Wenhua; Zhang, Cun-Hui
- The Annals of Statistics, Vol. 37, Issue 4
Fluorescent Protein Based FRET Pairs with Improved Dynamic Range for Fluorescence Lifetime Measurements
journal, August 2015
- George Abraham, Bobin; Sarkisyan, Karen S.; Mishin, Alexander S.
- PLOS ONE, Vol. 10, Issue 8
A Fast Global Fitting Algorithm for Fluorescence Lifetime Imaging Microscopy Based on Image Segmentation
journal, October 2004
- Pelet, S.; Previte, M. J. R.; Laiho, L. H.
- Biophysical Journal, Vol. 87, Issue 4
Robust Bayesian Fluorescence Lifetime Estimation, Decay Model Selection and Instrument Response Determination for Low-Intensity FLIM Imaging
journal, June 2016
- Rowley, Mark I.; Coolen, Anthonius C. C.; Vojnovic, Borivoj
- PLOS ONE, Vol. 11, Issue 6
05 billion events per second time correlated single photon counting using CMOS SPAD arrays
journal, January 2015
- Krstajić, Nikola; Poland, Simon; Levitt, James
- Optics Letters, Vol. 40, Issue 18
Two Modeling Strategies for Empirical Bayes Estimation
journal, May 2014
- Efron, Bradley
- Statistical Science, Vol. 29, Issue 2
siFLIM: single-image frequency-domain FLIM provides fast and photon-efficient lifetime data
journal, April 2016
- Raspe, Marcel; Kedziora, Katarzyna M.; van den Broek, Bram
- Nature Methods, Vol. 13, Issue 6
Accurate Analysis of Fluorescence Decays from Single Molecules in Photon Counting Experiments
journal, August 2003
- Turton, David A.; Reid, Gavin D.; Beddard, Godfrey S.
- Analytical Chemistry, Vol. 75, Issue 16
Penalized maximum likelihood estimation of lifetime and amplitude images from multi-exponentially decaying fluorescence signals
journal, January 2013
- Kim, Jeongtae; Seok, Jiyeong; Lee, Hwiin
- Optics Express, Vol. 21, Issue 17