1
|
Antarasen J, Wellnitz B, Kramer SN, Chatterjee S, Kisley L. Cross-correlation increases sampling in diffusion-based super-resolution optical fluctuation imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587586. [PMID: 38617244 PMCID: PMC11014504 DOI: 10.1101/2024.04.01.587586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Correlation signal processing of optical three-dimensional (x, y, t) data can produce super-resolution images. The second order cross-correlation function XC 2 has been documented to produce super-resolution imaging with static and blinking emitters but not for diffusing emitters. Here, we both analytically and numerically demonstrate cross-correlation analysis for diffusing particles. We then expand our fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) analysis to use cross-correlation as a post-processing computational technique to extract both dynamic and structural information of particle diffusion in nanoscale structures simultaneously. We further show how this method increases sampling rates and reduces aliasing for spatial information in both simulated and experimental data. Our work demonstrates how fcsSOFI with cross-correlation can be a powerful signal-processing tool to resolve the nanoscale dynamics and structure in samples relevant to biological and soft materials. TOC Graphic
Collapse
|
2
|
Alva A, Brito-Alarcón E, Linares A, Torres-García E, Hernández HO, Pinto-Cámara R, Martínez D, Hernández-Herrera P, D'Antuono R, Wood C, Guerrero A. Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start. J Microsc 2022; 288:218-241. [PMID: 35896096 PMCID: PMC10087389 DOI: 10.1111/jmi.13135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/27/2022]
Abstract
Due to the wave nature of light, optical microscopy has a lower-bound lateral resolution limit of approximately half of the wavelength of visible light, i.e., within the range of 200 to 350 nm. Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM) is a term used to encompass a collection of image analysis techniques which rely on the statistical processing of temporal variations of the fluorescence signal. FF-SRM aims to reduce the uncertainty of the location of fluorophores within an image, often improving spatial resolution to several tens of nanometers. FF-SRM is suitable for live-cell imaging due to its compatibility with most fluorescent probes and relatively simple instrumental and experimental requirements, which are mostly camera-based epifluorescence instruments. Each FF-SRM approach has strengths and weaknesses, which depend directly on the underlying statistical principles through which enhanced spatial resolution is achieved. In this review, the basic concepts and principles behind a range of FF-SRM methods published to date are described. Their operational parameters are explained and guidance for its selection is provided. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Alma Alva
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Eduardo Brito-Alarcón
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alejandro Linares
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Esley Torres-García
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Haydee O Hernández
- Posgrado en Ciencia e Ingeniería de la Computación, Universidad Nacional Autónoma de México, México City, México
| | - Raúl Pinto-Cámara
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.,Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Damián Martínez
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Paul Hernández-Herrera
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy Science and Technology Platform, The Francis Crick Institute, London, UK
| | - Christopher Wood
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adán Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| |
Collapse
|
3
|
Mukherjee S, Thomas C, Wilson R, Simmerman E, Hung ST, Jimenez R. Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances. Phys Chem Chem Phys 2022; 24:14310-14323. [DOI: 10.1039/d2cp00889k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states...
Collapse
|
4
|
Cevoli D, Vitale R, Vandenberg W, Hugelier S, Van den Eynde R, Dedecker P, Ruckebusch C. Design of experiments for the optimization of SOFI super-resolution microscopy imaging. BIOMEDICAL OPTICS EXPRESS 2021; 12:2617-2630. [PMID: 34123492 PMCID: PMC8176802 DOI: 10.1364/boe.421168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/15/2021] [Accepted: 03/29/2021] [Indexed: 05/04/2023]
Abstract
Super-resolution optical fluctuation imaging (SOFI) is a well-known super-resolution technique appreciated for its versatility and broad applicability. However, even though an extended theoretical description is available, it is still not fully understood how the interplay between different experimental parameters influences the quality of a SOFI image. We investigated the relationship between five experimental parameters (measurement time, on-time t on, off-time t off, probe brightness, and out of focus background) and the quality of the super-resolved images they yielded, expressed as Signal to Noise Ratio (SNR). Empirical relationships were modeled for second- and third-order SOFI using data simulated according to a D-Optimal design of experiments, which is an ad-hoc design built to reduce the experimental load when the total number of trials to be conducted becomes too high for practical applications. This approach proves to be more reliable and efficient for parameter optimization compared to the more classical parameter by parameter approach. Our results indicate that the best image quality is achieved for the fastest emitter blinking (lowest t on and t off), lowest background level, and the highest measurement duration, while the brightness variation does not affect the quality in a statistically significant way within the investigated range. However, when the ranges spanned by the parameters are constrained, a different set of optimal conditions may arise. For example, for second-order SOFI, we identified situations in which the increase of t off can be beneficial to SNR, such as when the measurement duration is long enough. In general, optimal values of t on and t off have been found to be highly dependent from each other and from the measurement duration.
Collapse
Affiliation(s)
- Dario Cevoli
- Univ. Lille, CNRS, LASIRE, Laboratory of advanced spectroscopy, interactions, reactivity and environment, F- 59000 Lille, France
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Raffaele Vitale
- Univ. Lille, CNRS, LASIRE, Laboratory of advanced spectroscopy, interactions, reactivity and environment, F- 59000 Lille, France
| | - Wim Vandenberg
- Univ. Lille, CNRS, LASIRE, Laboratory of advanced spectroscopy, interactions, reactivity and environment, F- 59000 Lille, France
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Siewert Hugelier
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Robin Van den Eynde
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Cyril Ruckebusch
- Univ. Lille, CNRS, LASIRE, Laboratory of advanced spectroscopy, interactions, reactivity and environment, F- 59000 Lille, France
| |
Collapse
|
5
|
Hugelier S, Vandenberg W, Lukeš T, Grußmayer KS, Eilers PHC, Dedecker P, Ruckebusch C. Smoothness correction for better SOFI imaging. Sci Rep 2021; 11:7569. [PMID: 33828326 PMCID: PMC8027426 DOI: 10.1038/s41598-021-87164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/23/2021] [Indexed: 12/02/2022] Open
Abstract
Sub-diffraction or super-resolution fluorescence imaging allows the visualization of the cellular morphology and interactions at the nanoscale. Statistical analysis methods such as super-resolution optical fluctuation imaging (SOFI) obtain an improved spatial resolution by analyzing fluorophore blinking but can be perturbed by the presence of non-stationary processes such as photodestruction or fluctuations in the illumination. In this work, we propose to use Whittaker smoothing to remove these smooth signal trends and retain only the information associated to independent blinking of the emitters, thus enhancing the SOFI signals. We find that our method works well to correct photodestruction, especially when it occurs quickly. The resulting images show a much higher contrast, strongly suppressed background and a more detailed visualization of cellular structures. Our method is parameter-free and computationally efficient, and can be readily applied on both two-dimensional and three-dimensional data.
Collapse
Affiliation(s)
| | - Wim Vandenberg
- Laboratory for Nanobiology, KU Leuven, 3001, Leuven, Belgium
| | - Tomáš Lukeš
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Kristin S Grußmayer
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland.,Grußmayer Lab, Delft University of Technology, 2629 HZ, Delft, the Netherlands
| | - Paul H C Eilers
- Erasmus University Medical Centre, 3015, Rotterdam, the Netherlands
| | - Peter Dedecker
- Laboratory for Nanobiology, KU Leuven, 3001, Leuven, Belgium
| | - Cyril Ruckebusch
- University of Lille, CNRS, UMR 8516, LASIRE, 59000, Lille, France
| |
Collapse
|
6
|
Tebo AG, Moeyaert B, Thauvin M, Carlon-Andres I, Böken D, Volovitch M, Padilla-Parra S, Dedecker P, Vriz S, Gautier A. Orthogonal fluorescent chemogenetic reporters for multicolor imaging. Nat Chem Biol 2020; 17:30-38. [PMID: 32778846 PMCID: PMC7610487 DOI: 10.1038/s41589-020-0611-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/02/2020] [Indexed: 12/24/2022]
Abstract
Spectrally separated fluorophores allow the observation of multiple targets simultaneously inside living cells, leading to a deeper understanding of the molecular interplay that regulates cell function and fate. Chemogenetic systems combining a tag and a synthetic fluorophore provide certain advantages over fluorescent proteins since there is no requirement for chromophore maturation. Here, we present the engineering of a set of spectrally orthogonal fluorogen activating tags based on the Fluorescence Activating and absorption Shifting Tag (FAST), that are compatible with two-color, live cell imaging. The resulting tags, greenFAST and redFAST, demonstrate orthogonality not only in their fluorogen recognition capabilities, but also in their one- and two-photon absorption profiles. This pair of orthogonal tags allowed the creation of a two-color cell cycle sensor capable of detecting very short, early cell cycles in zebrafish development, and the development of split complementation systems capable of detecting multiple protein-protein interactions by live cell fluorescence microscopy.
Collapse
Affiliation(s)
- Alison G Tebo
- Sorbonne University, École Normale Supérieure, PSL University, CNRS, Laboratoire des biomolécules (LBM), Paris, France.,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.,Janelia Farms Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Benjamien Moeyaert
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Marion Thauvin
- Center for Interdisciplinary Research, Collège de France, CNRS, INSERM, PSL University, Paris, France.,Sorbonne University, Paris, France
| | - Irene Carlon-Andres
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - Dorothea Böken
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Michel Volovitch
- Center for Interdisciplinary Research, Collège de France, CNRS, INSERM, PSL University, Paris, France.,Department of Biology, École Normale Supérieure, PSL University, Paris, France
| | - Sergi Padilla-Parra
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK.,Department of Infectious Diseases, Faculty of Life Sciences & Medicine, King's College London, London, UK.,Randall Centre for Cell and Molecular Biology, King's College London, London, UK
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Sophie Vriz
- Center for Interdisciplinary Research, Collège de France, CNRS, INSERM, PSL University, Paris, France.,Faculty of Sciences, Université de Paris, Paris, France
| | - Arnaud Gautier
- Sorbonne University, École Normale Supérieure, PSL University, CNRS, Laboratoire des biomolécules (LBM), Paris, France. .,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France. .,Institut Universitaire de France, Paris, France.
| |
Collapse
|
7
|
Grußmayer K, Lukes T, Lasser T, Radenovic A. Self-Blinking Dyes Unlock High-Order and Multiplane Super-Resolution Optical Fluctuation Imaging. ACS NANO 2020; 14:9156-9165. [PMID: 32567836 DOI: 10.1021/acsnano.0c04602] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Most diffraction-unlimited super-resolution imaging critically depends on the switching of fluorophores between at least two states, often induced using intense laser light and specialized buffers or UV radiation. Recently, so-called self-blinking dyes that switch spontaneously between an open, fluorescent "on" state and a closed, colorless "off" state were introduced. Here, we exploit the synergy between super-resolution optical fluctuation imaging (SOFI) and spontaneously switching fluorophores for 2D and 3D imaging. SOFI analyzes higher order statistics of fluctuations in the fluorophore emission instead of localizing individual molecules. It thereby tolerates a broad range of labeling densities, switching behavior, and probe brightness. Thus, even dyes that exhibit spontaneous blinking characteristics that are not suitable or suboptimal for single molecule localization microscopy can be used successfully for SOFI-based super-resolution imaging. We demonstrate 2D imaging of fixed cells with almost uniform resolution up to 50-60 nm in 6th order SOFI and characterize changing experimental conditions. Next, we investigate volumetric imaging using biplane and eight-plane data acquisition. We extend 3D cross-cumulant analysis to 4th order, achieving super-resolution in 3D with up to 29 depth planes. Finally, the low laser excitation intensities needed for single and biplane self-blinking SOFI are well suited for live-cell imaging. We show the perspective for time-resolved imaging by observing slow membrane movements in cells. Self-blinking SOFI thus provides a more robust alternative route for easy-to-use 2D and 3D high-resolution imaging.
Collapse
Affiliation(s)
- Kristin Grußmayer
- École Polytechnique Fédérale de Lausanne, Laboratory of Nanoscale Biology, 1015 Lausanne, Switzerland
| | - Tomas Lukes
- École Polytechnique Fédérale de Lausanne, Laboratory of Nanoscale Biology, 1015 Lausanne, Switzerland
| | - Theo Lasser
- École Polytechnique Fédérale de Lausanne, Laboratoire d'Optique Biomédicale, 1015 Lausanne, Switzerland
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Aleksandra Radenovic
- École Polytechnique Fédérale de Lausanne, Laboratory of Nanoscale Biology, 1015 Lausanne, Switzerland
| |
Collapse
|
8
|
Moeyaert B, Vandenberg W, Dedecker P. SOFIevaluator: a strategy for the quantitative quality assessment of SOFI data. BIOMEDICAL OPTICS EXPRESS 2020; 11:636-648. [PMID: 32133218 PMCID: PMC7041449 DOI: 10.1364/boe.382278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 05/21/2023]
Abstract
Super-resolution fluorescence imaging techniques allow optical imaging of specimens beyond the diffraction limit of light. Super-resolution optical fluctuation imaging (SOFI) relies on computational analysis of stochastic blinking events to obtain a super-resolved image. As with some other super-resolution methods, this strong dependency on computational analysis can make it difficult to gauge how well the resulting images reflect the underlying sample structure. We herein report SOFIevaluator, an unbiased and parameter-free algorithm for calculating a set of metrics that describes the quality of super-resolution fluorescence imaging data for SOFI. We additionally demonstrate how SOFIevaluator can be used to identify fluorescent proteins that perform well for SOFI imaging under different imaging conditions.
Collapse
Affiliation(s)
- Benjamien Moeyaert
- Laboratory for NanoBiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Wim Vandenberg
- Laboratory for NanoBiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Laboratory for NanoBiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| |
Collapse
|