1
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Bourauel L, Vaisband M, von der Emde L, Bermond K, Tarau IS, Heintzmann R, Holz FG, Curcio CA, Hasenauer J, Ach T. Spectral Analysis of Human Retinal Pigment Epithelium Cells in Healthy and AMD Eyes. Invest Ophthalmol Vis Sci 2024; 65:10. [PMID: 38170540 PMCID: PMC10768704 DOI: 10.1167/iovs.65.1.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Purpose Retinal pigment epithelium (RPE) cells show strong autofluorescence (AF). Here, we characterize the AF spectra of individual RPE cells in healthy eyes and those affected by age-related macular degeneration (AMD) and investigate associations between AF spectral response and the number of intracellular AF granules per cell. Methods RPE-Bruch's membrane flatmounts of 22 human donor eyes, including seven AMD-affected eyes (early AMD, three; geographic atrophy, one; neovascular, three) and 15 unaffected macula (<51 years, eight; >80 years, seven), were imaged at the fovea, perifovea, and near-periphery using confocal AF microscopy (excitation 488 nm), and emission spectra were recorded (500-710 nm). RPE cells were manually segmented with computer assistance and stratified by disease status, and emission spectra were analyzed using cubic spline transforms. Intracellular granules were manually counted and classified. Linear mixed models were used to investigate associations between spectra and the number of intracellular granules. Results Spectra of 5549 RPE cells were recorded. The spectra of RPE cells in healthy eyes showed similar emission curves that peaked at 580 nm for fovea and perifovea and at 575 and 580 nm for near-periphery. RPE spectral curves in AMD eyes differed significantly, being blue shifted by 10 nm toward shorter wavelengths. No significant association coefficients were found between wavelengths and granule counts. Conclusions This large series of RPE cell emission spectra at precisely predefined retinal locations showed a hypsochromic spectral shift in AMD. Combining different microscopy techniques, our work has identified cellular RPE spectral AF and subcellular granule properties that will inform future in vivo investigations using single-cell imaging.
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Affiliation(s)
- Leonie Bourauel
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Marc Vaisband
- Institute of Life & Medical Sciences, University of Bonn, Bonn, Germany
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Katharina Bermond
- Department of Ophthalmology, Ludwigshafen Hospital, Ludwigshafen, Germany
| | - Ioana Sandra Tarau
- Department of Ophthalmology, Asklepios Klinik Nord - Heidberg, Hamburg, Germany
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller University Jena, Jena, Germany
| | - Frank G. Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Christine A. Curcio
- Department of Ophthalmology, University of Alabama at Birmingham, Alabama, Alabama, United States
| | - Jan Hasenauer
- Institute of Life & Medical Sciences, University of Bonn, Bonn, Germany
| | - Thomas Ach
- Department of Ophthalmology, University of Bonn, Bonn, Germany
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2
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Pennacchietti F, Alvelid J, Morales RA, Damenti M, Ollech D, Oliinyk OS, Shcherbakova DM, Villablanca EJ, Verkhusha VV, Testa I. Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms. Nat Commun 2023; 14:8402. [PMID: 38114484 PMCID: PMC10730883 DOI: 10.1038/s41467-023-44054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Photolabeling of intracellular molecules is an invaluable approach to studying various dynamic processes in living cells with high spatiotemporal precision. Among fluorescent proteins, photoconvertible mechanisms and their products are in the visible spectrum (400-650 nm), limiting their in vivo and multiplexed applications. Here we report the phenomenon of near-infrared to far-red photoconversion in the miRFP family of near infrared fluorescent proteins engineered from bacterial phytochromes. This photoconversion is induced by near-infrared light through a non-linear process, further allowing optical sectioning. Photoconverted miRFP species emit fluorescence at 650 nm enabling photolabeling entirely performed in the near-infrared range. We use miRFPs as photoconvertible fluorescent probes to track organelles in live cells and in vivo, both with conventional and super-resolution microscopy. The spectral properties of miRFPs complement those of GFP-like photoconvertible proteins, allowing strategies for photoconversion and spectral multiplexed applications.
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Affiliation(s)
- Francesca Pennacchietti
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden.
| | - Jonatan Alvelid
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden
| | - Rodrigo A Morales
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, 17176, Sweden
- Center for Molecular Medicine (CMM), Stockholm, 17176, Sweden
| | - Martina Damenti
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden
| | - Dirk Ollech
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden
| | | | - Daria M Shcherbakova
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, 17176, Sweden
- Center for Molecular Medicine (CMM), Stockholm, 17176, Sweden
| | - Vladislav V Verkhusha
- Medicum, University of Helsinki, Helsinki, 00290, Finland
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ilaria Testa
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden.
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3
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Wang P, Kitano M, Keomanee-Dizon K, Truong TV, Fraser SE, Cutrale F. A single-shot hyperspectral phasor camera for fast, multi-color fluorescence microscopy. CELL REPORTS METHODS 2023; 3:100441. [PMID: 37159674 PMCID: PMC10162951 DOI: 10.1016/j.crmeth.2023.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/16/2022] [Accepted: 03/09/2023] [Indexed: 05/11/2023]
Abstract
Hyperspectral fluorescence imaging improves multiplexed observations of biological samples by utilizing multiple color channels across the spectral range to compensate for spectral overlap between labels. Typically, spectral resolution comes at a cost of decreased detection efficiency, which both hampers imaging speed and increases photo-toxicity to the samples. Here, we present a high-speed, high-efficiency snapshot spectral acquisition method, based on optical compression of the fluorescence spectra via Fourier transform, that overcomes the challenges of discrete spectral sampling: single-shot hyperspectral phasor camera (SHy-Cam). SHy-Cam captures fluorescence spatial and spectral information in a single exposure with a standard scientific CMOS camera, with photon efficiency of over 80%, easily and with acquisition rates exceeding 30 datasets per second, making it a powerful tool for multi-color in vivo imaging. Its simple design, using readily available optical components, and its easy integration provide a low-cost solution for multi-color fluorescence imaging with increased efficiency and speed.
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Affiliation(s)
- Pu Wang
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Masahiro Kitano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Kevin Keomanee-Dizon
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Thai V. Truong
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
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4
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Chiang HJ, Koo DES, Kitano M, Burkitt S, Unruh JR, Zavaleta C, Trinh LA, Fraser SE, Cutrale F. HyU: Hybrid Unmixing for longitudinal in vivo imaging of low signal-to-noise fluorescence. Nat Methods 2023; 20:248-258. [PMID: 36658278 PMCID: PMC9911352 DOI: 10.1038/s41592-022-01751-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/13/2022] [Indexed: 01/21/2023]
Abstract
The expansion of fluorescence bioimaging toward more complex systems and geometries requires analytical tools capable of spanning widely varying timescales and length scales, cleanly separating multiple fluorescent labels and distinguishing these labels from background autofluorescence. Here we meet these challenging objectives for multispectral fluorescence microscopy, combining hyperspectral phasors and linear unmixing to create Hybrid Unmixing (HyU). HyU is efficient and robust, capable of quantitative signal separation even at low illumination levels. In dynamic imaging of developing zebrafish embryos and in mouse tissue, HyU was able to cleanly and efficiently unmix multiple fluorescent labels, even in demanding volumetric timelapse imaging settings. HyU permits high dynamic range imaging, allowing simultaneous imaging of bright exogenous labels and dim endogenous labels. This enables coincident studies of tagged components, cellular behaviors and cellular metabolism within the same specimen, providing more accurate insights into the orchestrated complexity of biological systems.
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Affiliation(s)
- Hsiao Ju Chiang
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Daniel E S Koo
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Masahiro Kitano
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Sean Burkitt
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Cristina Zavaleta
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Le A Trinh
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Scott E Fraser
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, Los Angeles, CA, USA.
- Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA.
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5
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Díaz M, Malacrida L. Advanced Fluorescence Microscopy Methods to Study Dynamics of Fluorescent Proteins In Vivo. Methods Mol Biol 2023; 2564:53-74. [PMID: 36107337 DOI: 10.1007/978-1-0716-2667-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fluorescent proteins are standard tools for addressing biological questions in a cell biology laboratory. The genetic tagging of protein of interest with fluorescent proteins opens the opportunity to follow them in vivo and to understand their interactions and dynamics. In addition, the latest advances in optical microscopy image acquisition and processing allow us to study many cellular processes in vivo. Techniques such as fluorescence lifetime microscopy and hyperspectral imaging provide valuable tools for understanding fluorescent protein interactions and their photophysics. Finally, fluorescence fluctuation analysis opens the possibility to address questions of molecular diffusion, protein-protein interactions, and oligomerization, among others, yielding quantitative information on the subject of study. This chapter will cover some of the more important advances in cutting-edge technologies and methods that, combined with fluorescent proteins, open new frontiers for biological studies.
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Affiliation(s)
- Marcela Díaz
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo & Universidad de la República, Montevideo, Uruguay
| | - Leonel Malacrida
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo & Universidad de la República, Montevideo, Uruguay.
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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6
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Xue Y, Browne AW, Tang WC, Delgado J, McLelland BT, Nistor G, Chen JT, Chew K, Lee N, Keirstead HS, Seiler MJ. Retinal Organoids Long-Term Functional Characterization Using Two-Photon Fluorescence Lifetime and Hyperspectral Microscopy. Front Cell Neurosci 2021; 15:796903. [PMID: 34955757 PMCID: PMC8707055 DOI: 10.3389/fncel.2021.796903] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/26/2021] [Indexed: 12/31/2022] Open
Abstract
Pluripotent stem cell-derived organoid technologies have opened avenues to preclinical basic science research, drug discovery, and transplantation therapy in organ systems. Stem cell-derived organoids follow a time course similar to species-specific organ gestation in vivo. However, heterogeneous tissue yields, and subjective tissue selection reduce the repeatability of organoid-based scientific experiments and clinical studies. To improve the quality control of organoids, we introduced a live imaging technique based on two-photon microscopy to non-invasively monitor and characterize retinal organoids’ (RtOgs’) long-term development. Fluorescence lifetime imaging microscopy (FLIM) was used to monitor the metabolic trajectory, and hyperspectral imaging was applied to characterize structural and molecular changes. We further validated the live imaging experimental results with endpoint biological tests, including quantitative polymerase chain reaction (qPCR), single-cell RNA sequencing, and immunohistochemistry. With FLIM results, we analyzed the free/bound nicotinamide adenine dinucleotide (f/b NADH) ratio of the imaged regions and found that there was a metabolic shift from glycolysis to oxidative phosphorylation. This shift occurred between the second and third months of differentiation. The total metabolic activity shifted slightly back toward glycolysis between the third and fourth months and stayed relatively stable between the fourth and sixth months. Consistency in organoid development among cell lines and production lots was examined. Molecular analysis showed that retinal progenitor genes were expressed in all groups between days 51 and 159. Photoreceptor gene expression emerged around the second month of differentiation, which corresponded to the shift in the f/b NADH ratio. RtOgs between 3 and 6 months of differentiation exhibited photoreceptor gene expression levels that were between the native human fetal and adult retina gene expression levels. The occurrence of cone opsin expression (OPN1 SW and OPN1 LW) indicated the maturation of photoreceptors in the fourth month of differentiation, which was consistent with the stabilized level of f/b NADH ratio starting from 4 months. Endpoint single-cell RNA and immunohistology data showed that the cellular compositions and lamination of RtOgs at different developmental stages followed those in vivo.
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Affiliation(s)
- Yuntian Xue
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States.,Stem Cell Research Center, University of California, Irvine, Irvine, CA, United States
| | - Andrew W Browne
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States.,Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States.,Institute for Clinical and Translational Science, University of California, Irvine, Irvine, CA, United States
| | - William C Tang
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Jeffrey Delgado
- Stem Cell Research Center, University of California, Irvine, Irvine, CA, United States
| | | | | | - Jacqueline T Chen
- Stem Cell Research Center, University of California, Irvine, Irvine, CA, United States.,Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States
| | - Kaylee Chew
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Nicolas Lee
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | | | - Magdalene J Seiler
- Stem Cell Research Center, University of California, Irvine, Irvine, CA, United States.,Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States.,Department of Physical Medicine & Rehabilitation, University of California, Irvine, Irvine, CA, United States.,Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA, United States
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7
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Malacrida L, Ranjit S, Jameson DM, Gratton E. The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation. Annu Rev Biophys 2021; 50:575-593. [PMID: 33957055 DOI: 10.1146/annurev-biophys-062920-063631] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phasor approach to fluorescence lifetime imaging has become a common method to analyze complicated fluorescence signals from biological samples. The appeal of the phasor representation of complex fluorescence decays in biological systems is that a visual representation of the decay of entire cells or tissues can be used to easily interpret fundamental biological states related to metabolism and oxidative stress. Phenotyping based on autofluorescence provides new avenues for disease characterization and diagnostics. The phasor approach is a transformation of complex fluorescence decays that does not use fits to model decays and therefore has the same information content as the original data. The phasor plot is unique for a given system, is highly reproducible, and provides a robust method to evaluate the existence of molecular interactions such as Förster resonance energy transfer or the response of ion indicators. Recent advances permitquantification of multiple components from phasor plots in fluorescence lifetime imaging microscopy, which is not presently possible using data fitting methods, especially in biological systems.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay.,Advanced Bioimaging Unit, Institut Pasteur Montevideo and Universidad de la República-Uruguay, 11400 Montevideo, Uruguay
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
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8
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Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging. Nat Methods 2021; 18:542-550. [PMID: 33859440 PMCID: PMC10161785 DOI: 10.1038/s41592-021-01108-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 03/03/2021] [Indexed: 02/02/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) and spectral imaging are two broadly applied methods for increasing dimensionality in microscopy. However, their combination is typically inefficient and slow in terms of acquisition and processing. By integrating technological and computational advances, we developed a robust and unbiased spectral FLIM (S-FLIM) system. Our method, Phasor S-FLIM, combines true parallel multichannel digital frequency domain electronics with a multidimensional phasor approach to extract detailed and precise information about the photophysics of fluorescent specimens at optical resolution. To show the flexibility of the Phasor S-FLIM technology and its applications to the biological and biomedical field, we address four common, yet challenging, problems: the blind unmixing of spectral and lifetime signatures from multiple unknown species, the unbiased bleedthrough- and background-free Förster resonance energy transfer analysis of biosensors, the photophysical characterization of environment-sensitive probes in living cells and parallel four-color FLIM imaging in tumor spheroids.
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9
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Franssen WMJ, Vergeldt FJ, Bader AN, van Amerongen H, Terenzi C. Full-Harmonics Phasor Analysis: Unravelling Multiexponential Trends in Magnetic Resonance Imaging Data. J Phys Chem Lett 2020; 11:9152-9158. [PMID: 33053305 PMCID: PMC7649845 DOI: 10.1021/acs.jpclett.0c02319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phasor analysis is a robust, nonfitting, method for the study of multiexponential decays in lifetime imaging data, routinely used in Fluorescence Lifetime Imaging Microscopy (FLIM) and only recently validated for Magnetic Resonance Imaging (MRI). In the established phasor approach, typically only the first Fourier harmonic is used to unravel time-domain exponential trends and their intercorrelations across image voxels. Here, we demonstrate the potential of full-harmonics (FH) phasor analysis by using all frequency-domain data points in simulations and quantitative MRI (qMRI) T2 measurements of phantoms with bulk liquids or liquid-filled porous particles and of a human brain. We show that FH analysis, while of limited advantage in FLIM due to the correlated nature of shot noise, in MRI outperforms single-harmonic phasor in unravelling multiple physical environments and partial-volume effects otherwise undiscernible. We foresee application of FH phasor to, e.g., big-data analysis in qMRI of biological or other multiphase systems, where multiparameter fitting is unfeasible.
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Affiliation(s)
- Wouter M. J. Franssen
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
| | - Frank J. Vergeldt
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
| | - Arjen N. Bader
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
- MicroSpectroscopy
Centre, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Herbert van Amerongen
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
- MicroSpectroscopy
Centre, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Camilla Terenzi
- Laboratory
of Biophysics, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
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10
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Shi W, Koo DES, Kitano M, Chiang HJ, Trinh LA, Turcatel G, Steventon B, Arnesano C, Warburton D, Fraser SE, Cutrale F. Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations. Nat Commun 2020; 11:726. [PMID: 32024828 PMCID: PMC7002680 DOI: 10.1038/s41467-020-14486-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/12/2020] [Indexed: 11/09/2022] Open
Abstract
Hyperspectral fluorescence imaging is gaining popularity for it enables multiplexing of spatio-temporal dynamics across scales for molecules, cells and tissues with multiple fluorescent labels. This is made possible by adding the dimension of wavelength to the dataset. The resulting datasets are high in information density and often require lengthy analyses to separate the overlapping fluorescent spectra. Understanding and visualizing these large multi-dimensional datasets during acquisition and pre-processing can be challenging. Here we present Spectrally Encoded Enhanced Representations (SEER), an approach for improved and computationally efficient simultaneous color visualization of multiple spectral components of hyperspectral fluorescence images. Exploiting the mathematical properties of the phasor method, we transform the wavelength space into information-rich color maps for RGB display visualization. We present multiple biological fluorescent samples and highlight SEER’s enhancement of specific and subtle spectral differences, providing a fast, intuitive and mathematical way to interpret hyperspectral images during collection, pre-processing and analysis. Spectral phasor analysis allows unmixing fluorescence microscopy images, but it requires user involvement and has a limited number of labels that can be analyzed and displayed. Here the authors present a semi-automated solution to visualise multiple spectral components of hyperspectral fluorescence images, simultaneously.
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Affiliation(s)
- Wen Shi
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Daniel E S Koo
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Masahiro Kitano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Hsiao J Chiang
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Le A Trinh
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Gianluca Turcatel
- Developmental Biology and Regenerative Medicine Program, Saban Research Institute, Children's Hospital, 4661 Sunset Blvd, Los Angeles, CA, 90089, USA.,Keck School of Medicine and Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Benjamin Steventon
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Cosimo Arnesano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - David Warburton
- Developmental Biology and Regenerative Medicine Program, Saban Research Institute, Children's Hospital, 4661 Sunset Blvd, Los Angeles, CA, 90089, USA.,Keck School of Medicine and Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Scott E Fraser
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA. .,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA. .,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.
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11
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Abstract
Embryonic development is highly complex and dynamic, requiring the coordination of numerous molecular and cellular events at precise times and places. Advances in imaging technology have made it possible to follow developmental processes at cellular, tissue, and organ levels over time as they take place in the intact embryo. Parallel innovations of in vivo probes permit imaging to report on molecular, physiological, and anatomical events of embryogenesis, but the resulting multidimensional data sets pose significant challenges for extracting knowledge. In this review, we discuss recent and emerging advances in imaging technologies, in vivo labeling, and data processing that offer the greatest potential for jointly deciphering the intricate cellular dynamics and the underlying molecular mechanisms. Our discussion of the emerging area of “image-omics” highlights both the challenges of data analysis and the promise of more fully embracing computation and data science for rapidly advancing our understanding of biology.
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Affiliation(s)
- Francesco Cutrale
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
| | - Scott E. Fraser
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
- Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Le A. Trinh
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
- Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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12
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Sediqi H, Wray A, Jones C, Jones M. Application of Spectral Phasor analysis to sodium microenvironments in myoblast progenitor cells. PLoS One 2018; 13:e0204611. [PMID: 30379959 PMCID: PMC6209149 DOI: 10.1371/journal.pone.0204611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022] Open
Abstract
Sodium ions (Na+) are key regulators of molecular events in many cellular processes, yet the dynamics of this ion remain poorly defined. Developing approaches to identify and characterise Na+ microenvironments will enable more detailed elucidation of the mechanisms of signal transduction. Here we report the application of Spectral Phasor analysis to the Na+ fluorophore, CoroNa Green, to identify and spatially map spectral emissions that report Na+ microenvironments. We use differentiating stem cells where Na+ fluxes were reported as an antecedent. Myoblast stem cells were induced to differentiate by serum starvation and then fixed at intervals between 0 and 40-minutes of differentiation prior to addition of CoroNa Green. The fluorescent intensity was insufficient to identify discrete Na+ microenvironments. However, using Spectral Phasor analysis we identified spectral shifts in CoroNa Green fluorescence which is related to the Na+ microenvironment. Further, spectral-heterogeneity appears to be contingent on the distance of Na+ from the nucleus in the early stages of differentiation. Spectral Phasor analysis of CoroNa Green in fixed stem cells demonstrates for the first time that CoroNa Green has unique spectral emissions depending on the nature of the Na+ environment in differentiating stem cells. Applying Spectral Phasor analysis to CoroNa Green in live stem cells is likely to further elucidate the role of Na+ microenvironments in the differentiation process.
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Affiliation(s)
- Hamid Sediqi
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Alex Wray
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Christopher Jones
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Mark Jones
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
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13
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Dvornikov A, Gratton E. Hyperspectral imaging in highly scattering media by the spectral phasor approach using two filters. BIOMEDICAL OPTICS EXPRESS 2018; 9:3503-3511. [PMID: 30338135 PMCID: PMC6191637 DOI: 10.1364/boe.9.003503] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/14/2018] [Accepted: 06/18/2018] [Indexed: 05/25/2023]
Abstract
Hyperspectral imaging is a common technique in fluorescence microscopy to obtain the emission spectrum at each pixel of an image. However, methods to obtain spectral resolution based on diffraction gratings or integrated prisms work poorly when the sample is strongly scattering. We developed a microscope named the DIVER that collects the fluorescence emission over a very large angle. Since the fluorescence light after passing through the multiple scattering sample is not collimated, the use of grating or prisms strongly limits the amount of light that can be used with available hyperspectral devices. Here we show that 2 filters that accept uncollimated light over a large aperture are sufficient to calculate the spectral phasor rather than displaying the entire spectrum. Using the properties of the spectral phasors, we can resolve spectral components and perform the type of data analyses that are usually performed in hyperspectral image analysis.
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Affiliation(s)
- Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697, USA
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14
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Fereidouni F, Griffin C, Todd A, Levenson R. Multispectral analysis tools can increase utility of RGB color images in histology. JOURNAL OF OPTICS (2010) 2018; 20:044007. [PMID: 30847052 PMCID: PMC6398595 DOI: 10.1088/2040-8986/aab0e8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Multispectral imaging (MSI) is increasingly finding application in the study and characterization of biological specimens. However, the methods typically used come with challenges on both the acquisition and the analysis front. MSI can be slow and photon-inefficient, leading to long imaging times and possible phototoxicity and photobleaching. The resulting datasets can be large and complex, prompting the development of a number of mathematical approaches for segmentation and signal unmixing. We show that under certain circumstances, just three spectral channels provided by standard color cameras, coupled with multispectral analysis tools, including a more recent spectral phasor approach, can efficiently provide useful insights. These findings are supported with a mathematical model relating spectral bandwidth and spectral channel number to achievable spectral accuracy. The utility of 3-band RGB and MSI analysis tools are demonstrated on images acquired using brightfield and fluorescence techniques, as well as a novel microscopy approach employing UV-surface excitation. Supervised linear unmixing, automated non-negative matrix factorization and phasor analysis tools all provide useful results, with phasors generating particularly helpful spectral display plots for sample exploration.
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Affiliation(s)
- Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817, United States of America
| | - Croix Griffin
- School of Veterinary Medicine, University of California Davis, 944 Garrod Drive, Davis, CA 95616, United States of America
| | - Austin Todd
- Department of Pathology and Laboratory Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817, United States of America
| | - Richard Levenson
- Department of Pathology and Laboratory Medicine, University of California Davis, 4400 V Street, Sacramento, CA 95817, United States of America
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15
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Browne AW, Arnesano C, Harutyunyan N, Khuu T, Martinez JC, Pollack HA, Koos DS, Lee TC, Fraser SE, Moats RA, Aparicio JG, Cobrinik D. Structural and Functional Characterization of Human Stem-Cell-Derived Retinal Organoids by Live Imaging. Invest Ophthalmol Vis Sci 2017; 58:3311-3318. [PMID: 28672397 PMCID: PMC5495152 DOI: 10.1167/iovs.16-20796] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Purpose Human pluripotent stem cell (hPSC)-derived retinal organoids are a platform for investigating retinal development, pathophysiology, and cellular therapies. In contrast to histologic analysis in which multiple specimens fixed at different times are used to reconstruct developmental processes, repeated analysis of the same living organoids provides a more direct means to characterize changes. New live imaging modalities can provide insights into retinal organoid structure and metabolic function during in vitro growth. This study employed live tissue imaging to characterize retinal organoid development, including metabolic changes accompanying photoreceptor differentiation. Methods Live hPSC-derived retinal organoids at different developmental stages were examined for microanatomic organization and metabolic function by phase contrast microscopy, optical coherence tomography (OCT), fluorescence lifetime imaging microscopy (FLIM), and hyperspectral imaging (HSpec). Features were compared to those revealed by histologic staining, immunostaining, and microcomputed tomography (micro-CT) of fixed organoid tissue. Results We used FLIM and HSpec to detect changes in metabolic activity as organoids differentiated into organized lamellae. FLIM detected increased glycolytic activity and HSpec detected retinol and retinoic acid accumulation in the organoid outer layer, coinciding with photoreceptor genesis. OCT enabled imaging of lamellae formed during organoid maturation. Micro-CT revealed three-dimensional structure, but failed to detect lamellae. Conclusions Live imaging modalities facilitate real-time and nondestructive imaging of retinal organoids as they organize into lamellar structures. FLIM and HSpec enable rapid detection of lamellar structure and photoreceptor metabolism. Live imaging techniques may aid in the continuous evaluation of retinal organoid development in diverse experimental and cell therapy settings.
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Affiliation(s)
- Andrew W Browne
- USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
| | - Cosimo Arnesano
- Translational Imaging Center, University of Southern California, Los Angeles, California, United States 3Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States
| | - Narine Harutyunyan
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Thien Khuu
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Juan Carlos Martinez
- USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
| | - Harvey A Pollack
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, United States 6Department of Radiology, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - David S Koos
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, United States 6Department of Radiology, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Thomas C Lee
- USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States 4The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - Scott E Fraser
- Translational Imaging Center, University of Southern California, Los Angeles, California, United States 3Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States 5The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, United States 7Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, United States
| | - Rex A Moats
- The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, United States 6Department of Radiology, Children's Hospital Los Angeles, Los Angeles, California, United States 7Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, United States
| | - Jennifer G Aparicio
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California, United States
| | - David Cobrinik
- USC Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States 4The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California, United States 5The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California, United States 8Department of Biochemistry & Molecular Medicine, and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California, United States
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16
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Scipioni L, Gratton E, Diaspro A, Lanzanò L. Phasor Analysis of Local ICS Detects Heterogeneity in Size and Number of Intracellular Vesicles. Biophys J 2017; 111:619-629. [PMID: 27508445 PMCID: PMC4982927 DOI: 10.1016/j.bpj.2016.06.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/09/2016] [Accepted: 06/22/2016] [Indexed: 01/28/2023] Open
Abstract
Organelles represent the scale of organization immediately below that of the cell itself, and their composition, size, and number are tailored to their function. Monitoring the size and number of organelles in live cells is relevant for many applications but can be challenging due to their highly heterogeneous properties. Image correlation spectroscopy is a well-established analysis method capable of extracting the average size and number of particles in images. However, when image correlation spectroscopy is applied to a highly heterogeneous system, it can fail to retrieve, from a single correlation function, the characteristic size and the relative amount associated to each subspecies. Here, we describe a fast, unbiased, and fit-free algorithm based on the phasor analysis of multiple local image correlation functions, capable of mapping the sizes of elements contained in a heterogeneous system. The method correctly provides the size and number of separate subspecies, which otherwise would be hidden in the average properties of a single correlation function. We apply the method to quantify the spatial and temporal heterogeneity in the size and number of intracellular vesicles formed after endocytosis in live cells.
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Affiliation(s)
- Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Computer Science, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, Italy
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, California
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, Genoa, Italy; Nikon Imaging Center, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy
| | - Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, Genoa, Italy.
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17
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Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging. Nat Methods 2017; 14:149-152. [PMID: 28068315 DOI: 10.1038/nmeth.4134] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/08/2016] [Indexed: 11/09/2022]
Abstract
Time-lapse imaging of multiple labels is challenging for biological imaging as noise, photobleaching and phototoxicity compromise signal quality, while throughput can be limited by processing time. Here, we report software called Hyper-Spectral Phasors (HySP) for denoising and unmixing multiple spectrally overlapping fluorophores in a low signal-to-noise regime with fast analysis. We show that HySP enables unmixing of seven signals in time-lapse imaging of living zebrafish embryos.
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18
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Cao R, Jenkins P, Peria W, Sands B, Naivar M, Brent R, Houston JP. Phasor plotting with frequency-domain flow cytometry. OPTICS EXPRESS 2016; 24:14596-607. [PMID: 27410612 PMCID: PMC5025209 DOI: 10.1364/oe.24.014596] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/14/2016] [Accepted: 06/04/2016] [Indexed: 05/23/2023]
Abstract
Interest in time resolved flow cytometry is growing. In this paper, we collect time-resolved flow cytometry data and use it to create polar plots showing distributions that are a function of measured fluorescence decay rates from individual fluorescently-labeled cells and fluorescent microspheres. Phasor, or polar, graphics are commonly used in fluorescence lifetime imaging microscopy (FLIM). In FLIM measurements, the plotted points on a phasor graph represent the phase-shift and demodulation of the frequency-domain fluorescence signal collected by the imaging system for each image pixel. Here, we take a flow cytometry cell counting system, introduce into it frequency-domain optoelectronics, and process the data so that each point on a phasor plot represents the phase shift and demodulation of an individual cell or particle. In order to demonstrate the value of this technique, we show that phasor graphs can be used to discriminate among populations of (i) fluorescent microspheres, which are labeled with one fluorophore type; (ii) Chinese hamster ovary (CHO) cells labeled with one and two different fluorophore types; and (iii) Saccharomyces cerevisiae cells that express combinations of fluorescent proteins with different fluorescence lifetimes. The resulting phasor plots reveal differences in the fluorescence lifetimes within each sample and provide a distribution from which we can infer the number of cells expressing unique single or dual fluorescence lifetimes. These methods should facilitate analysis time resolved flow cytometry data to reveal complex fluorescence decay kinetics.
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Affiliation(s)
- Ruofan Cao
- Department of Chemical and Materials Engineering, New Mexico State University, MSC 3805, PO BOX 30001, 1040 South Horseshoe Drive, Las Cruces, NM 88003,
USA
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi,
China
- Bioinspired Engineering and Biomechanics Center, Xi'an Jiaotong University, Xi'an, Shanxi,
China
| | - Patrick Jenkins
- Department of Chemical and Materials Engineering, New Mexico State University, MSC 3805, PO BOX 30001, 1040 South Horseshoe Drive, Las Cruces, NM 88003,
USA
| | - William Peria
- Fred Hutchinson Cancer Research Center, Seattle, WA,
USA
| | - Bryan Sands
- Fred Hutchinson Cancer Research Center, Seattle, WA,
USA
| | | | - Roger Brent
- Fred Hutchinson Cancer Research Center, Seattle, WA,
USA
| | - Jessica P. Houston
- Department of Chemical and Materials Engineering, New Mexico State University, MSC 3805, PO BOX 30001, 1040 South Horseshoe Drive, Las Cruces, NM 88003,
USA
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19
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Leray A, Brulé T, Buret M, Colas des Francs G, Bouhelier A, Dereux A, Finot E. Sorting of Single Biomolecules based on Fourier Polar Representation of Surface Enhanced Raman Spectra. Sci Rep 2016; 6:20383. [PMID: 26833130 PMCID: PMC4735853 DOI: 10.1038/srep20383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/31/2015] [Indexed: 12/29/2022] Open
Abstract
Surface enhanced Raman scattering (SERS) spectroscopy becomes increasingly used in biosensors for its capacity to detect and identify single molecules. In practice, a large number of SERS spectra are acquired and reliable ranking methods are thus essential for analysing all these data. Supervised classification strategies, which are the most effective methods, are usually applied but they require pre-determined models or classes. In this work, we propose to sort SERS spectra in unknown groups with an alternative strategy called Fourier polar representation. This non-fitting method based on simple Fourier sine and cosine transforms produces a fast and graphical representation for sorting SERS spectra with quantitative information. The reliability of this method was first investigated theoretically and numerically. Then, its performances were tested on two concrete biological examples: first with single amino-acid molecule (cysteine) and then with a mixture of three distinct odorous molecules. The benefits of this Fourier polar representation were highlighted and compared to the well-established statistical principal component analysis method.
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Affiliation(s)
- Aymeric Leray
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université Bourgogne Franche-Comté, 21000 Dijon (France)
| | - Thibault Brulé
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université Bourgogne Franche-Comté, 21000 Dijon (France)
| | - Mickael Buret
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université Bourgogne Franche-Comté, 21000 Dijon (France)
| | - Gérard Colas des Francs
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université Bourgogne Franche-Comté, 21000 Dijon (France)
| | - Alexandre Bouhelier
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université Bourgogne Franche-Comté, 21000 Dijon (France)
| | - Alain Dereux
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université Bourgogne Franche-Comté, 21000 Dijon (France)
| | - Eric Finot
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université Bourgogne Franche-Comté, 21000 Dijon (France)
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20
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Trinh LA, Fraser SE. Imaging the Cell and Molecular Dynamics of Craniofacial Development: Challenges and New Opportunities in Imaging Developmental Tissue Patterning. Curr Top Dev Biol 2015; 115:599-629. [PMID: 26589939 DOI: 10.1016/bs.ctdb.2015.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The development of the vertebrate head requires cell-cell and tissue-tissue interactions between derivatives of the three germ layers to coordinate morphogenetic movements in four dimensions (4D: x, y, z, t). The high spatial and temporal resolution offered by optical microscopy has made it the main imaging modularity for capturing the molecular and cellular dynamics of developmental processes. In this chapter, we highlight the challenges and new opportunities provided by emerging technologies that enable dynamic, high-information-content imaging of craniofacial development. We discuss the challenges of varying spatial and temporal scales encountered from the biological and technological perspectives. We identify molecular and fluorescence imaging technology that can provide solutions to some of the challenges. Application of the techniques described within this chapter combined with considerations of the biological and technical challenges will aid in formulating the best image-based studies to extend our understanding of the genetic and environmental influences underlying craniofacial anomalies.
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Affiliation(s)
- Le A Trinh
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Scott E Fraser
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
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21
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Chen H, Gratton E, Digman MA. Spectral properties and dynamics of gold nanorods revealed by EMCCD-based spectral phasor method. Microsc Res Tech 2015; 78:283-93. [PMID: 25684346 PMCID: PMC4404027 DOI: 10.1002/jemt.22473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 01/17/2015] [Indexed: 11/12/2022]
Abstract
Gold nanorods (NRs) with tunable plasmon-resonant absorption in the near-infrared region have considerable advantages over organic fluorophores as imaging agents due to their brightness and lack of photobleaching. However, the luminescence spectral properties of NRs have not been fully characterized at the single particle level due to lack of proper analytic tools. Here, we present a spectral phasor analysis method that allows investigations of NRs' spectra at single particle level showing the spectral variance and providing spatial information during imaging. The broad phasor distribution obtained by the spectral phasor analysis indicates that spectra of NRs are different from particle to particle. NRs with different spectra can be identified in images with high spectral resolution. The spectral behaviors of NRs under different imaging conditions, for example, different excitation powers and wavelengths, were revealed by our laser-scanning multiphoton microscope using a high-resolution spectrograph with imaging capability. Our results prove that the spectral phasor method is an easy and efficient tool in hyper-spectral imaging analysis to unravel subtle changes of the emission spectrum. We applied this method to study the spectral dynamics of NRs during direct optical trapping and by optothermal trapping. Interestingly, different spectral shifts were observed in both trapping phenomena.
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Affiliation(s)
- Hongtao Chen
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine
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