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Single-Molecule Localization Microscopy  •  Software Benchmarking

  • Second edition of the challenge in SMLMS 2016

  • Publication of the results in Nature Methods 2015

  • The 2013 Challenge is turned to an online permanent challenge

  • Super-resolution microscopy wins the 2014 Nobel Prize

  • Open software initiative for bioimaging informatics

Benchmarking of SMLM Software

Comprehensive review of the single-molecule localization microscopy (SMLM, PALM, STORM) software packages.
This benchmarking uses common reference datasets that simulates biological structures and image formation process. The evaluation of the software packages is performed with well-defined metrics to get an objective and quantitative assessment. The performance test is mainly done be the developers of the software themselves who participate to a challenge.

Super-resolution microscopy wins the 2014 Nobel Prize in Chemistry


Super-resolution fluorescence microscopy is an emerging multidisciplinary field that has opened up new opportunities in studying the living cell at the nanometer scale. It overcomes the classical diffraction limit of Abbe, yielding images of biological structures that have lateral resolution down to 10 nm. One of the most promising techniques in this field is single molecule localization. It was announced Method of the Year 2008 by the Nature Methods journal [1] and was was recognized with the 2014 Nobel Prize in chemistry [2]. This technique has been gaining growing attention in microscopy, biology, and engineering conferences, among them ISBI, ever since. The method is based on exciting a spatially sparse set of fluorophores at each time instant, and on fitting the acquired images with a PSF (point spread function) model. This technique was originally proposed and introduced by three independent groups in 2006, giving rise to several acronyms: PALM (photo-activated localization microscopy by Eric Betzig et al.), STORM (stochastic optical reconstruction microscopy by Xiaowei Zhuang et al.), and F-PALM (fluorescence PALM by Samuel Hess). Unlike classical fluorescence microscopy, however, the acquired data cannot be visualized and inspected directly, and an additional processing step is required in this regard. The algorithmic aspects of the single molecule method are therefore extremely important, and this is the focus of the challenge we propose here.

Computational reconstruction by image-analysis software packages

There are currently numerous image-analysis software packages that process super resolution data. A typical data set consists of millions of excited fluorophores, distributed over thousands of images. The excited fluorophores are then detected, localized and visualized by these software tools. Automation is an indispensable aspect of the method [3] and a challenging task [4], as the data is very long image sequence.



2nd round10 April 2017

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.

Live Workshop28 August 2016

28 Aug: Special Session
» Live TV YouTube Channel

Participation1 August 2016

A large panel of software have submitted localization files to the challenge in all modalities.

Competition is running15 June 2016

The competition Challenge 2016 will run from 15 June to 22 July 2016. The results will be presented SMLMS 2016 symposium in Lausanne Switzerland, 28-30th August.

Dataset (3D)6 May 2016

The first dataset is released. The same sample is simulated in 4 modalities: 2D, 3D-astigmatism, 3D-biplane, and 3D-double-helix.

fight club
26 Feb. 2016

Seamus Holden and Daniel Sage
Nature Photonics 10, 2016, PDF.

New challenge 24 Aug. 2015

A new challenge will be held in August 2016. Send an email to be kept informed.

Publication 15 June 2015

Advanced online publication of the comparative results on the Nature Methods website.

Software 24 Jan. 2015

Update of the comprehensive list of SMLM software packages. 45 for localization software and 6 for deconvolution-type reconstruction software.

Conditions of use 27 Sept. 2014

These reference datasets are designed to be largely used by the developpers to validate theirs software and by the users to check a software. They can be freely used if the sources and references are properly cited.

Online challenge 11 July 2013

The ISBI Challenge is turned to a permanent online challenge.

© 2017 Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 31 Mar 2017