Quantitative evaluation of software packages for single-molecule localization microscopy

被引：0

作者：

Sage, Daniel ^{[1
]}

Kirshner, Hagai ^{[1
]}

Pengo, Thomas ^{[2
]}

Stuurman, Nico ^{[3
,4
]}

Min, Junhong ^{[5
]}

Manley, Suliana ^{[6
]}

Unser, Michael ^{[1
]}

机构：

[1] Ecole Polytech Fed Lausanne, Biomed Imaging Grp, CH-1015 Lausanne, Switzerland

[2] Ctr Genom Regulat, Barcelona, Spain

[3] Univ Calif UCSF, Howard Hughes Med Inst, San Francisco, CA USA

[4] Univ Calif San Francisco, Dept Cellular & Mol Pharmacol, San Francisco, CA 94143 USA

[5] Korea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Taejon 305701, South Korea

[6] Ecole Polytech Fed Lausanne, Lab Expt Biophys, CH-1015 Lausanne, Switzerland

来源：

NATURE METHODS | 2015年 / 12卷 / 08期

基金：

欧洲研究理事会;

关键词：

SUPERRESOLUTION MICROSCOPY; FLUORESCENCE MICROSCOPY; DIFFRACTION-LIMIT; RADIAL SYMMETRY; IMAGE-ANALYSIS; RESOLUTION; RECONSTRUCTION; ALGORITHM; ACCURACY; TRACKING;

D O I：

10.1038/NMETH.3442

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution microscopy and present a comprehensive evaluation of localization software packages. Our philosophy is to evaluate each package as a whole, thus maintaining the integrity of the software. We prepared synthetic data that represent three-dimensional structures modeled after biological components, taking excitation parameters, noise sources, point-spread functions and pixelation into account. We then asked developers to run their software on our data; most responded favorably, allowing us to present a broad picture of the methods available. We evaluated their results using quantitative and user-interpretable criteria: detection rate, accuracy, quality of image reconstruction, resolution, software usability and computational resources. These metrics reflect the various tradeoffs of SMLM software packages and help users to choose the software that fits their needs.

引用

页码：717 / U37

页数：12

共 66 条

[1] Quantitative study of single molecule location estimation techniques [J].

Abraham, Anish V. ;

Ram, Sripad ;

Chao, Jerry ;

Ward, E. S. ;

Ober, Raimund J. .

OPTICS EXPRESS, 2009, 17 (26) :23352-23373

[2] Localization of a fluorescent source without numerical fitting [J].

Andersson, Sean B. .

OPTICS EXPRESS, 2008, 16 (23) :18714-18724

[3] Image Analysis with Rapid and Accurate Two-Dimensional Gaussian Fitting [J].

Anthony, Stephen M. ;

Granick, Steve .

LANGMUIR, 2009, 25 (14) :8152-8160

[4] A high-density 3D localization algorithm for stochastic optical reconstruction microscopy [J].

Babcock, Hazen ;

Sigal, Yaron M. ;

Zhuang, Xiaowei .

Optical Nanoscopy, 2012, 1 (01) :1-10

[5] Fast compressed sensing analysis for super-resolution imaging using L1-homotopy [J].

Babcock, Hazen P. ;

Moffitt, Jeffrey R. ;

Cao, Yunlong ;

Zhuang, Xiaowei .

OPTICS EXPRESS, 2013, 21 (23) :28583-28596

[6] Visualization of Localization Microscopy Data [J].

Baddeley, David ;

Cannell, Mark B. ;

Soeller, Christian .

MICROSCOPY AND MICROANALYSIS, 2010, 16 (01) :64-72

[7] Plasmonics Meets Far-Field Optical Nanoscopy [J].

Balzarotti, Francisco ;

Stefani, Fernando D. .

ACS NANO, 2012, 6 (06) :4580-4584

[8] Fourier ring correlation as a resolution criterion for super-resolution microscopy [J].

Banterle, Niccolo ;

Khanh Huy Bui ;

Lemke, Edward A. ;

Beck, Martin .

JOURNAL OF STRUCTURAL BIOLOGY, 2013, 183 (03) :363-367

[9]

Bennett K., 2014, 4 SINGL MOL LOC MICR

[10] Imaging intracellular fluorescent proteins at nanometer resolution [J].

Betzig, Eric ;

Patterson, George H. ;

Sougrat, Rachid ;

Lindwasser, O. Wolf ;

Olenych, Scott ;

Bonifacino, Juan S. ;

Davidson, Michael W. ;

Lippincott-Schwartz, Jennifer ;

Hess, Harald F. .

SCIENCE, 2006, 313 (5793) :1642-1645

← 1 2 3 4 5 6 7 →