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Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
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Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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2
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Barbotin A, Galiani S, Urbančič I, Eggeling C, Booth MJ. Adaptive optics allows STED-FCS measurements in the cytoplasm of living cells. OPTICS EXPRESS 2019; 27:23378-23395. [PMID: 31510616 PMCID: PMC6825603 DOI: 10.1364/oe.27.023378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 05/18/2023]
Abstract
Fluorescence correlation spectroscopy in combination with super-resolution stimulated emission depletion microscopy (STED-FCS) is a powerful tool to investigate molecular diffusion with sub-diffraction resolution. It has been of particular use for investigations of two dimensional systems like cell membranes, but has so far seen very limited applications to studies of three-dimensional diffusion. One reason for this is the extreme sensitivity of the axial (z) STED depletion pattern to optical aberrations. We present here an adaptive optics-based correction method that compensates for these aberrations and allows STED-FCS measurements in the cytoplasm of living cells.
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Affiliation(s)
- Aurélien Barbotin
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ,
UK
| | - Silvia Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
| | - Iztok Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
- “Jožef Stefan” Institute, Jamova cesta 39, SI-1000 Ljubljana,
Slovenia
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS,
UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena,
Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745 Jena,
Germany
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ,
UK
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Ng XW, Sampath K, Wohland T. Fluorescence Correlation and Cross-Correlation Spectroscopy in Zebrafish. Methods Mol Biol 2019; 1863:67-105. [PMID: 30324593 DOI: 10.1007/978-1-4939-8772-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
There has been increasing interest in biophysical studies on live organisms to gain better insights into physiologically relevant biological events at the molecular level. Zebrafish (Danio rerio) is a viable vertebrate model to study such events due to its genetic and evolutionary similarities to humans, amenability to less invasive fluorescence techniques owing to its transparency and well-characterized genetic manipulation techniques. Fluorescence techniques used to probe biomolecular dynamics and interactions of molecules in live zebrafish embryos are therefore highly sought-after to bridge molecular and developmental events. Fluorescence correlation and cross-correlation spectroscopy (FCS and FCCS) are two robust techniques that provide molecular level information on dynamics and interactions respectively. Here, we detail the steps for applying confocal FCS and FCCS, in particular single-wavelength FCCS (SW-FCCS), in live zebrafish embryos, beginning with sample preparation, instrumentation, calibration, and measurements on the FCS/FCCS instrument and ending with data analysis.
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Affiliation(s)
- Xue Wen Ng
- Department of Chemistry and Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Karuna Sampath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Thorsten Wohland
- Department of Chemistry and Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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Khadem SMJ, Hille C, Löhmannsröben HG, Sokolov IM. Spot variation fluorescence correlation spectroscopy by data post-processing. Sci Rep 2017; 7:5614. [PMID: 28717215 PMCID: PMC5514068 DOI: 10.1038/s41598-017-05672-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/26/2017] [Indexed: 11/09/2022] Open
Abstract
Spot variation fluorescence correlation spectroscopy (SV-FCS) is a variant of the FCS techniques which may give useful information about the structural organisation of the medium in which the diffusion takes place. We show that the same results can be obtained by post-processing the photon count data from ordinary FCS measurements. By using this method, one obtains the fluorescence autocorrelation functions for sizes of confocal volume, which are effectively smaller than that of the initial FCS measurement. The photon counts of the initial experiment are first transformed into smooth intensity trace using kernel smoothing method or to a piecewise-continuous intensity trace using binning and then a non-linear transformation is applied to this trace. The result of this transformation mimics the photon count rate in an experiment performed with a smaller confocal volume. The applicability of the method is established in extensive numerical simulations and directly supported in in-vitro experiments. The procedure is then applied to the diffusion of AlexaFluor647-labeled streptavidin in living cells.
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Affiliation(s)
- S M J Khadem
- Humboldt University Berlin, Institute of Physics, Berlin, D-12489, Germany. .,Humboldt University Berlin, School of Analytical Sciences Adlershof (SALSA), Berlin, D-12489, Germany.
| | - C Hille
- University of Potsdam, Institute of Chemistry, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - H-G Löhmannsröben
- Humboldt University Berlin, School of Analytical Sciences Adlershof (SALSA), Berlin, D-12489, Germany.,University of Potsdam, Institute of Chemistry, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - I M Sokolov
- Humboldt University Berlin, Institute of Physics, Berlin, D-12489, Germany.,Humboldt University Berlin, School of Analytical Sciences Adlershof (SALSA), Berlin, D-12489, Germany
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Gallagher J, Delon A, Moreau P, Wang I. Optimizing the metric in sensorless adaptive optical microscopy with fluorescence fluctuations. OPTICS EXPRESS 2017; 25:15558-15571. [PMID: 28788978 DOI: 10.1364/oe.25.015558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Adaptive optics (AO) strategies using optimization-based, sensorless approaches are widely used, especially for microscopy applications. To converge rapidly to the best correction, such approaches require that a quality metric and a set of modes be chosen optimally. Fluorescence fluctuations microscopy, a family of methods that provides quantitative measurements of molecular concentration and mobility in living specimen, is in particular need of adaptive optics, since its results can be strongly biased by optical aberrations. We examined two possible metrics for sensorless AO, measured in a solution of fluorophores diffusing in 3D: the fluorescence count rate and the molecular brightness (or number of photons detected per molecule in the observation volume). We studied their respective measurement noise and sensitivity to aberrations. Then, AO correction accuracy was experimentally assessed by measuring the residual aberration after correcting a known wavefront. We proposed a theoretical framework to predict the correction accuracy, knowing the metric measurement noise and sensitivity. In the small aberration range, the brightness allows more accurate corrections when fluorophores are few but bright, whereas the count rate performs better in more concentrated solutions. When correcting large aberrations, the count rate is expected to be a more reliable metric.
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Lagerholm BC, Andrade DM, Clausen MP, Eggeling C. Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:063001. [PMID: 28458397 PMCID: PMC5390782 DOI: 10.1088/1361-6463/aa519e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/15/2016] [Accepted: 12/05/2016] [Indexed: 05/06/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s-1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1-10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of ≈0.7-1.0 µm2 s-1, and a compartment size of about 100-150 nm.
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Affiliation(s)
- B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Débora M Andrade
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford OX1 3SR, UK
| | - Mathias P Clausen
- MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Christian Eggeling
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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Leroux CE, Monnier S, Wang I, Cappello G, Delon A. Fluorescent correlation spectroscopy measurements with adaptive optics in the intercellular space of spheroids. BIOMEDICAL OPTICS EXPRESS 2014; 5:3730-8. [PMID: 25360385 PMCID: PMC4206337 DOI: 10.1364/boe.5.003730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 05/06/2023]
Abstract
In this study we demonstrate the use of adaptive optics to correct the biasing effects of optical aberrations when measuring the dynamics of molecules diffusing between cells in multicellular spheroids. Our results indicate that, on average, adaptive optics leads to a reduction of the 3D size of the point spread function that is statistically significant in terms of measured number of molecules and diffusion time. The sensorless approach, which uses the molecular brightness as optimization metric, is validated in a complex, highly heterogeneous, biological environment. This work paves the way towards the design of accurate diffusion measurements of molecules in thick biological specimens.
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Affiliation(s)
- Charles-Edouard Leroux
- Univ. Grenoble Alpes, LIPHY, F-38000 Grenoble, France
- CNRS, LIPHY, F-38000 Grenoble, France
- Institut Langevin, ESPCI ParisTech, CNRS, 1 rue Jussieu, 75238 Paris Cedex 05, France
| | - Sylvain Monnier
- UMR 168, Institut Curie, Centre de Recherche, 26 rue d’Ulm 75005 Paris, France
| | - Irène Wang
- Univ. Grenoble Alpes, LIPHY, F-38000 Grenoble, France
- CNRS, LIPHY, F-38000 Grenoble, France
| | - Giovanni Cappello
- Univ. Grenoble Alpes, LIPHY, F-38000 Grenoble, France
- CNRS, LIPHY, F-38000 Grenoble, France
| | - Antoine Delon
- Univ. Grenoble Alpes, LIPHY, F-38000 Grenoble, France
- CNRS, LIPHY, F-38000 Grenoble, France
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Leroux CE, Grichine A, Wang I, Delon A. Correction of cell-induced optical aberrations in a fluorescence fluctuation microscope. OPTICS LETTERS 2013; 38:2401-3. [PMID: 23939061 PMCID: PMC3967118 DOI: 10.1364/ol.38.002401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We describe the effect of optical aberrations on fluorescence fluctuations microscopy (FFM), when focusing through a single living cell. FFM measurements are performed in an aqueous fluorescent solution and prove to be a highly sensitive tool to assess the optical aberrations introduced by the cell. We demonstrate an adaptive optics (AO) system to remove the aberration-related bias in the FFM measurements. Our data show that AO is not only useful when imaging deep in tissues but also when performing FFM measurements through a single cellular layer. This work paves the way for the application of FFM to complex three-dimensional multicellular samples.
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Affiliation(s)
- Charles-Edouard Leroux
- Institut Langevin "ondes et images"
CNRS : UMR7587ESPCI ParisTechUniversité Pierre et Marie Curie (UPMC) - Paris VIUniversité Paris VII - Paris Diderot10 Rue Vauquelin 75231 Paris Cedex 05, FR
| | - Alexei Grichine
- Institut d'oncologie/développement Albert Bonniot de Grenoble
INSERM : U823CHU GrenobleEFSUniversité Joseph Fourier - Grenoble IInstitut Albert Bonniot, BP170, 38042 Grenoble Cedex 9, FR
| | - Irène Wang
- LIPhy, Laboratoire Interdisciplinaire de Physique
CNRS : UMR5588Université Joseph Fourier - Grenoble I FR
| | - Antoine Delon
- LIPhy, Laboratoire Interdisciplinaire de Physique
CNRS : UMR5588Université Joseph Fourier - Grenoble I FR
- * Correspondence should be addressed to: Antoine Delon
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