Quantitative Evaluation of Software Packages for Single-Molecule Localization Microscopy
D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, M. Unser
Nature Methods—Techniques for Life Scientists and Chemists, vol. 12, no. 8, pp. 717-724, August 2015.
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.
AUTHOR="Sage, D. and Kirshner, H. and Pengo, T. and Stuurman, N. and
Min, J. and Manley, S. and Unser, M.",
TITLE="Quantitative Evaluation of Software Packages for Single-Molecule
JOURNAL="Nature Methods---Techniques for Life Scientists and Chemists",
Nature Publishing Group.
Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from
Nature Publishing Group.
This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.