1
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Faklaris O, Bancel-Vallée L, Dauphin A, Monterroso B, Frère P, Geny D, Manoliu T, de Rossi S, Cordelières FP, Schapman D, Nitschke R, Cau J, Guilbert T. Quality assessment in light microscopy for routine use through simple tools and robust metrics. J Biophys Biochem Cytol 2022; 221:213512. [PMID: 36173380 PMCID: PMC9526251 DOI: 10.1083/jcb.202107093] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 04/04/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Although there is a need to demonstrate reproducibility in light microscopy acquisitions, the lack of standardized guidelines monitoring microscope health status over time has so far impaired the widespread use of quality control (QC) measurements. As scientists from 10 imaging core facilities who encounter various types of projects, we provide affordable hardware and open source software tools, rigorous protocols, and define reference values to assess QC metrics for the most common fluorescence light microscopy modalities. Seven protocols specify metrics on the microscope resolution, field illumination flatness, chromatic aberrations, illumination power stability, stage drift, positioning repeatability, and spatial-temporal noise of camera sensors. We designed the MetroloJ_QC ImageJ/Fiji Java plugin to incorporate the metrics and automate analysis. Measurements allow us to propose an extensive characterization of the QC procedures that can be used by any seasoned microscope user, from research biologists with a specialized interest in fluorescence light microscopy through to core facility staff, to ensure reproducible and quantifiable microscopy results.
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Affiliation(s)
- Orestis Faklaris
- Montpellier Ressources Imagerie, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Leslie Bancel-Vallée
- Montpellier Ressources Imagerie, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Aurélien Dauphin
- Unite Genetique et Biologie du Développement U934, PICT-IBiSA, Institut Curie, INSERM, CNRS, PSL Research University, Paris, France
| | - Baptiste Monterroso
- Prism, Institut de Biologie Valrose, CNRS UMR 7277, INSERM 1091, University of Nice Sophia Antipolis - Parc Valrose, Nice, France
| | - Perrine Frère
- Plate-forme d'Imagerie de Tenon, UMR_S 1155, Hôpital Tenon, Paris, France
| | - David Geny
- Institut de Psychiatrie Et Neurosciences de Paris, INSERM U1266, Paris, France
| | - Tudor Manoliu
- Gustave Roussy, Université Paris-Saclay, Plate-forme Imagerie et Cytométrie, UMS AMMICa. Villejuif, France
| | - Sylvain de Rossi
- Montpellier Ressources Imagerie, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Fabrice P Cordelières
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, UMS 3420, US 4, Bordeaux, France
| | - Damien Schapman
- Université of Rouen Normandie, INSERM, Plate-Forme de Recherche en Imagerie Cellulaire de Normandie, Rouen, France
| | - Roland Nitschke
- Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University Freiburg, Freiburg, Germany
| | - Julien Cau
- Montpellier Ressources Imagerie, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Thomas Guilbert
- Institut Cochin, INSERM (U1016), CNRS (UMR 8104), Universite de Paris (UMR-S1016), Paris, France
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2
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Ryan DP, Dunlap MK, Gelfand MP, Werner JH, Van Orden AK, Goodwin PM. A gain series method for accurate EMCCD calibration. Sci Rep 2021; 11:18348. [PMID: 34526588 PMCID: PMC8443689 DOI: 10.1038/s41598-021-97759-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/27/2021] [Indexed: 11/09/2022] Open
Abstract
Calibration of the gain and digital conversion factor of an EMCCD is necessary for accurate photon counting. We present a new method to quickly calibrate multiple gain settings of an EMCCD camera. Acquiring gain-series calibration data and analyzing the resulting images with the EMCCD noise model more accurately estimates the gain response of the camera. Furthermore, we develop a method to compare the results from different calibration approaches. Gain-series calibration outperforms all other methods in this self-consistency test.
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Affiliation(s)
- Duncan P Ryan
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, 87545, USA.
| | - Megan K Dunlap
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
| | - Martin P Gelfand
- Department of Physics, Colorado State University, Fort Collins, CO, 80523, USA
| | - James H Werner
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, 87545, USA
| | - Alan K Van Orden
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
| | - Peter M Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, 87545, USA
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3
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Brenner B, Song KH, Sun C, Zhang HF. Improving spatial precision and field-of-view in wavelength-tagged single-particle tracking using spectroscopic single-molecule localization microscopy. APPLIED OPTICS 2021; 60:3647-3658. [PMID: 33983297 PMCID: PMC8648066 DOI: 10.1364/ao.415275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/30/2021] [Indexed: 05/09/2023]
Abstract
Spectroscopic single-molecule localization microscopy (sSMLM) generates super-resolution images of single molecules while simultaneously capturing the spectra of their fluorescence emissions. However, sSMLM splits photons from single-molecule emissions into a spatial channel and a spectral channel, reducing both channels' precisions. It is also challenging in transmission grating-based sSMLM to achieve a large field-of-view (FOV) and avoid overlap between the spatial and spectral channels. The challenge in FOV has further significance in single-molecule tracking applications. In this work, we analyzed the correlation between the spatial and spectral channels in sSMLM to improve its spatial precision, and we developed a split-mirror assembly to enlarge its FOV. We demonstrate the benefits of these improvements by tracking quantum dots. We also show that we can reduce particle-identification ambiguity by tagging each particle with its unique spectral characteristics.
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Affiliation(s)
- Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA
| | - Ki-Hee Song
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA
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4
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Zhang Z, Wang Y, Piestun R, Huang ZL. Characterizing and correcting camera noise in back-illuminated sCMOS cameras. OPTICS EXPRESS 2021; 29:6668-6690. [PMID: 33726183 DOI: 10.1364/oe.418684] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
With promising properties of fast imaging speed, large field-of-view, relative low cost and many others, back-illuminated sCMOS cameras have been receiving intensive attention for low light level imaging in the past several years. However, due to the pixel-to-pixel difference of camera noise (called noise non-uniformity) in sCMOS cameras, researchers may hesitate to use them in some application fields, and sometimes wonder whether they should optimize the noise non-uniformity of their sCMOS cameras before using them in a specific application scenario. In this paper, we systematically characterize the impact of different types of sCMOS noise on image quality and perform corrections to these types of sCMOS noise using three representative algorithms (PURE, NCS and MLEsCMOS). We verify that it is possible to use appropriate correction methods to push the non-uniformity of major types of camera noise, including readout noise, offset, and photon response, to a satisfactory level for conventional microscopy and single molecule localization microscopy. We further find out that, after these corrections, global read noise becomes a major concern that limits the imaging performance of back-illuminated sCMOS cameras. We believe this study provides new insights into the understanding of camera noise in back-illuminated sCMOS cameras, and also provides useful information for future development of this promising camera technology.
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5
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Li M, Huang ZL. Rethinking resolution estimation in fluorescence microscopy: from theoretical resolution criteria to super-resolution microscopy. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1776-1785. [PMID: 33351176 DOI: 10.1007/s11427-020-1785-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
Resolution is undoubtedly the most important parameter in optical microscopy by providing an estimation on the maximum resolving power of a certain optical microscope. For centuries, the resolution of an optical microscope is generally considered to be limited only by the numerical aperture of the optical system and the wavelength of light. However, since the invention and popularity of various advanced fluorescence microscopy techniques, especially super-resolution fluorescence microscopy, many new methods have been proposed for estimating the resolution, leading to confusions for researchers who need to quantify the resolution of their fluorescence microscopes. In this paper, we firstly summarize the early concepts and criteria for predicting the resolution limit of an ideal optical system. Then, we discuss some important influence factors that deteriorate the resolution of a certain fluorescence microscope. Finally, we provide methods and examples on how to measure the resolution of a fluorescence microscope from captured fluorescence images. This paper aims to answer as best as possible the theoretical and practical issues regarding the resolution estimation in fluorescence microscopy.
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Affiliation(s)
- Mengting Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhen-Li Huang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China. .,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, 430074, China. .,School of Biomedical Engineering, Hainan University, Haikou, 570228, China.
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6
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Song KH, Zhang Y, Brenner B, Sun C, Zhang HF. Symmetrically dispersed spectroscopic single-molecule localization microscopy. LIGHT, SCIENCE & APPLICATIONS 2020; 9:92. [PMID: 32509299 PMCID: PMC7248114 DOI: 10.1038/s41377-020-0333-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/02/2020] [Accepted: 05/11/2020] [Indexed: 05/09/2023]
Abstract
Spectroscopic single-molecule localization microscopy (sSMLM) was used to achieve simultaneous imaging and spectral analysis of single molecules for the first time. Current sSMLM fundamentally suffers from a reduced photon budget because the photons from individual stochastic emissions are divided into spatial and spectral channels. Therefore, both spatial localization and spectral analysis only use a portion of the total photons, leading to reduced precisions in both channels. To improve the spatial and spectral precisions, we present symmetrically dispersed sSMLM, or SDsSMLM, to fully utilize all photons from individual stochastic emissions in both spatial and spectral channels. SDsSMLM achieved 10-nm spatial and 0.8-nm spectral precisions at a total photon budget of 1000. Compared with the existing sSMLM using a 1:3 splitting ratio between spatial and spectral channels, SDsSMLM improved the spatial and spectral precisions by 42% and 10%, respectively, under the same photon budget. We also demonstrated multicolour imaging of fixed cells and three-dimensional single-particle tracking using SDsSMLM. SDsSMLM enables more precise spectroscopic single-molecule analysis in broader cell biology and material science applications.
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Affiliation(s)
- Ki-Hee Song
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208 USA
| | - Yang Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208 USA
| | - Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208 USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208 USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208 USA
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7
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Song KH, Dong B, Sun C, Zhang HF. Theoretical analysis of spectral precision in spectroscopic single-molecule localization microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:123703. [PMID: 30599574 PMCID: PMC6289825 DOI: 10.1063/1.5054144] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Spectroscopic single-molecule localization microscopy (sSMLM) is a novel super-resolution imaging technology, which simultaneously records the nanoscopic location and the corresponding full emission spectrum of every stochastic single-molecule emission event. This spectroscopic imaging capability of sSMLM necessitates the establishment of a theoretical foundation of the newly introduced spectral precision and to guide the system design and optimization. Based on numerical simulation and analytical solution, we introduced such a theoretical model to analyze spectral precision by considering the main system parameters, including signal and background shot noises, readout noise, and the spectral calibration procedure. Using this model, we demonstrated the delicate balance among these parameters in achieving the optimal spectral precision and discovered that the best spectral precision can only be achieved at a particular system spectral dispersion. For example, with a given signal of 3000 photons and a readout noise of 2 e-, a system spectral dispersion of 1.6 nm/pixel is required for sSMLM to achieve the highest spectral precision of 1.31 nm.
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Affiliation(s)
- Ki-Hee Song
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Biqin Dong
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Author to whom correspondence should be addressed:
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8
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Copeland CR, Geist J, McGray CD, Aksyuk VA, Liddle JA, Ilic BR, Stavis SM. Subnanometer localization accuracy in widefield optical microscopy. LIGHT, SCIENCE & APPLICATIONS 2018; 7:31. [PMID: 30839614 PMCID: PMC6107003 DOI: 10.1038/s41377-018-0031-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/24/2018] [Accepted: 05/01/2018] [Indexed: 05/16/2023]
Abstract
The common assumption that precision is the limit of accuracy in localization microscopy and the typical absence of comprehensive calibration of optical microscopes lead to a widespread issue-overconfidence in measurement results with nanoscale statistical uncertainties that can be invalid due to microscale systematic errors. In this article, we report a comprehensive solution to this underappreciated problem. We develop arrays of subresolution apertures into the first reference materials that enable localization errors approaching the atomic scale across a submillimeter field. We present novel methods for calibrating our microscope system using aperture arrays and develop aberration corrections that reach the precision limit of our reference materials. We correct and register localization data from multiple colors and test different sources of light emission with equal accuracy, indicating the general applicability of our reference materials and calibration methods. In a first application of our new measurement capability, we introduce the concept of critical-dimension localization microscopy, facilitating tests of nanofabrication processes and quality control of aperture arrays. In a second application, we apply these stable reference materials to answer open questions about the apparent instability of fluorescent nanoparticles that commonly serve as fiducial markers. Our study establishes a foundation for subnanometer localization accuracy in widefield optical microscopy.
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Affiliation(s)
- Craig R. Copeland
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
- Maryland NanoCenter, University of Maryland, College Park, MD 20742 USA
| | - Jon Geist
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Craig D. McGray
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Vladimir A. Aksyuk
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - J. Alexander Liddle
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - B. Robert Ilic
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Samuel M. Stavis
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
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9
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Wang Y, Zhao L, Hu Z, Wang Y, Zhao Z, Li L, Huang ZL. Quantitative performance evaluation of a back-illuminated sCMOS camera with 95% QE for super-resolution localization microscopy. Cytometry A 2017; 91:1175-1183. [PMID: 29165899 DOI: 10.1002/cyto.a.23282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/29/2017] [Accepted: 10/18/2017] [Indexed: 11/07/2022]
Abstract
Scientific Complementary Metal Oxide Semiconductor (sCMOS) cameras were introduced into the market in 2009 and are now becoming a major type of commercial cameras for low-light imaging. sCMOS cameras provide simultaneously low read noise, high readout speed, and large pixel array; however, the relatively low quantum efficiency (QE) of sCMOS cameras has been a major limitation for its application in single molecule imaging, especially super-resolution localization microscopy which requires high detection sensitivity. Here we report the imaging performance of a newly released back-illuminated sCMOS camera (called Dhyana 95 from Tucsen) which is claimed to be the world's first 95% QE sCMOS camera. The imaging performance evaluation is based on a new methodology which is designed to provide paired images from two tested cameras under almost identical experimental conditions. We verified that this new 95% QE sCMOS camera is able to provide superior imaging performance over a representative front-illuminated sCMOS camera (Hamamatsu Flash 4.0 V2) and a popular back-illuminated EMCCD camera (Andor iXon 897 Ultra) in a wide signal range. We hope this study will inspire more studies on using sCMOS cameras in super-resolution localization microscopy, or even single molecule imaging. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Yujie Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Lingxi Zhao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Zhe Hu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yina Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Zeyu Zhao
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Luchang Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Zhen-Li Huang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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10
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Ma H, Xu J, Jin J, Huang Y, Liu Y. A Simple Marker-Assisted 3D Nanometer Drift Correction Method for Superresolution Microscopy. Biophys J 2017; 112:2196-2208. [PMID: 28538156 DOI: 10.1016/j.bpj.2017.04.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 11/15/2022] Open
Abstract
High-precision fluorescence microscopy such as superresolution imaging or single-particle tracking often requires an online drift correction method to maintain the stability of the three-dimensional (3D) position of the sample at a nanometer precision throughout the entire data acquisition process. Current online drift correction methods require modification of the existing two-dimensional (2D) fluorescence microscope with additional optics and detectors, which can be cumbersome and limit its use in many biological laboratories. Here we report a simple marker-assisted online drift correction method in which all 3D positions can be derived from fiducial markers on the coverslip of the sample on a standard 2D fluorescence microscope without additional optical components. We validate this method by tracking the long-term 3D stability of single-molecule localization microscopy at a precision of <2 and 5 nm in the lateral and axial dimension, respectively. We then provide three examples to evaluate the performance of the marker-assisted drift correction method. Finally, we give an example of a biological application of superresolution imaging of spatiotemporal alteration for a DNA replication structure with both low-abundance newly synthesized DNAs at the early onset of DNA synthesis and gradually condensed DNA structures during DNA replication. Using an isogenic breast cancer progression cell line model that recapitulates normal-like, precancerous, and tumorigenic stages, we characterize a distinction in the DNA replication process in normal, precancerous, and tumorigenic cells.
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Affiliation(s)
- Hongqiang Ma
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jianquan Xu
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jingyi Jin
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania; School of Medicine, Tsinghua University, Haidian District, Beijing, China
| | - Yi Huang
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Yang Liu
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania; University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania.
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11
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McGray C, Copeland CR, Stavis SM, Geist J. Centroid precision and orientation precision of planar localization microscopy. J Microsc 2016; 263:238-49. [PMID: 26970565 PMCID: PMC11025010 DOI: 10.1111/jmi.12384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/09/2016] [Indexed: 11/27/2022]
Abstract
The concept of localization precision, which is essential to localization microscopy, is formally extended from optical point sources to microscopic rigid bodies. Measurement functions are presented to calculate the planar pose and motion of microscopic rigid bodies from localization microscopy data. Physical lower bounds on the associated uncertainties - termed centroid precision and orientation precision - are derived analytically in terms of the characteristics of the optical measurement system and validated numerically by Monte Carlo simulations. The practical utility of these expressions is demonstrated experimentally by an analysis of the motion of a microelectromechanical goniometer indicated by a sparse constellation of fluorescent nanoparticles. Centroid precision and orientation precision, as developed here, are useful concepts due to the generality of the expressions and the widespread interest in localization microscopy for super-resolution imaging and particle tracking.
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Affiliation(s)
- C McGray
- Engineering Physics Division, NIST, Gaithersburg, Maryland, U.S.A
- Modern Microsystems, Silver Spring, Maryland, U.S.A
| | - C R Copeland
- Center for Nanoscale Science and Technology, NIST, Gaithersburg, Maryland, U.S.A
- Maryland Nanocenter, University of Maryland, College Park, Maryland, U.S.A
| | - S M Stavis
- Center for Nanoscale Science and Technology, NIST, Gaithersburg, Maryland, U.S.A
| | - J Geist
- Engineering Physics Division, NIST, Gaithersburg, Maryland, U.S.A
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12
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Chen X, Zeng Z, Li R, Xue B, Xi P, Sun Y. Superior performance with sCMOS over EMCCD in super-resolution optical fluctuation imaging. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:66007. [PMID: 27281064 DOI: 10.1117/1.jbo.21.6.066007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/10/2016] [Indexed: 06/06/2023]
Abstract
Super-resolution optical fluctuation imaging (SOFI) is a fast and low-cost live-cell optical nanoscopy for extracting subdiffraction information from the statistics of fluorescence intensity fluctuation. As SOFI is based on the fluctuation statistics, rather than the detection of single molecules, it poses unique requirements for imaging detectors, which still lack a systematic evaluation. Here, we analyze the influences of pixel sizes, frame rates, noise levels, and different gains in SOFI with simulations and experimental tests. Our analysis shows that the smaller pixel size and faster readout speed of scientific-grade complementary metal oxide semiconductor (sCMOS) enables SOFI to achieve high spatiotemporal resolution with a large field-of-view, which is especially beneficial for live-cell super-resolution imaging. Overall, as the performance of SOFI is relatively insensitive to the signal-to-noise ratio (SNR), the gain in pixel size and readout speed exceeds the loss in SNR, indicating sCMOS is superior to electron multiplying charge coupled device in context to SOFI in many cases. Super-resolution imaging of cellular microtubule structures with high-order SOFI is experimentally demonstrated at large field-of-view, taking advantage of the large pixel number and fast frame rate of sCMOS cameras.
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Affiliation(s)
- Xuanze Chen
- Peking University, College of Engineering, Department of Biomedical Engineering, No. 5 Yiheyuan Road Haidian District, Beijing 100871, ChinabPeking University, State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of
| | - Zhiping Zeng
- Peking University, College of Engineering, Department of Biomedical Engineering, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Rongqin Li
- Peking University, State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Boxin Xue
- Peking University, State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Peng Xi
- Peking University, College of Engineering, Department of Biomedical Engineering, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Yujie Sun
- Peking University, State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
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Siraj N, El-Zahab B, Hamdan S, Karam TE, Haber LH, Li M, Fakayode SO, Das S, Valle B, Strongin RM, Patonay G, Sintim HO, Baker GA, Powe A, Lowry M, Karolin JO, Geddes CD, Warner IM. Fluorescence, Phosphorescence, and Chemiluminescence. Anal Chem 2015; 88:170-202. [PMID: 26575092 DOI: 10.1021/acs.analchem.5b04109] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Noureen Siraj
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Bilal El-Zahab
- Department of Mechanical and Materials Engineering, Florida International University , Miami, Florida 33174, United States
| | - Suzana Hamdan
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Tony E Karam
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Louis H Haber
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Min Li
- Process Development Center, Albemarle Corporation , Baton Rouge, Louisiana 70805, United States
| | - Sayo O Fakayode
- Department of Chemistry, Winston-Salem State University , Winston-Salem, North Carolina 27110, United States
| | - Susmita Das
- Department of Civil Engineering, Adamas Institute of Technology , Barasat, Kolkata 700126, West Bengal India
| | - Bertha Valle
- Department of Chemistry, Texas Southern University , Houston, Texas 77004, United States
| | - Robert M Strongin
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Gabor Patonay
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-4098, United States
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri Columbia , Columbia, Missouri 65211-7600, United States
| | - Aleeta Powe
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40208, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Jan O Karolin
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Chris D Geddes
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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Hirvonen LM, Kilfeather T, Suhling K. Single-molecule localization software applied to photon counting imaging. APPLIED OPTICS 2015; 54:5074-5082. [PMID: 26192667 DOI: 10.1364/ao.54.005074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Centroiding in photon counting imaging has traditionally been accomplished by a single-step, noniterative algorithm, often implemented in hardware. Single-molecule localization techniques in superresolution fluorescence microscopy are conceptually similar, but use more sophisticated iterative software-based fitting algorithms to localize the fluorophore. Here, we discuss common features and differences between single-molecule localization and photon counting imaging and investigate the suitability of single-molecule localization software for photon event localization. We find that single-molecule localization software packages designed for superresolution microscopy-QuickPALM, rapidSTORM, and ThunderSTORM-can work well when applied to photon counting imaging with a microchannel-plate-based intensified camera system: photon event recognition can be excellent, fixed pattern noise can be low, and the microchannel plate pores can easily be resolved.
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