Benchmarking of SMLM Software
Comprehensive review of the single-molecule localization microscopy (SMLM, PALM, STORM) software packages.
NATURE METHODS | ANALYSIS
D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley & M. Unser, Quantitative evaluation of software packages for single-molecule localization microscopy, Nature Methods (2015). doi:10.1038/nmeth.3442
Abstract 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.
Thanh-an Pham has a talk at the SMLMS 2017 Symposium in London: Developments of the ongoing 3D SMLM software challenge.
Update of the directory of SMLM software packages. 83 SMLM software are now identified and referred.
From April 10 to May 10 a second round of the challenge is running. All the DH have be submitted
with the new normalized datasets.
A large panel of software have submitted localization files to the challenge in all modalities.
The first dataset is released. The same sample is simulated in 4 modalities: 2D, 3D-astigmatism, 3D-biplane, and 3D-double-helix.
A new challenge will be held in August 2016. Send an email to be kept informed.
Advanced online publication of the comparative results on the Nature Methods website.
The ISBI Challenge is turned to a permanent online challenge.
Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 31 Mar 2017