Single-Molecule Localization Microscopy  •  Software Benchmarking

  • Second edition of the challenge presented at SMLMS 2016

  • Special session on YouTube

  • Super-resolution fight club

  • Publication of the results in Nature Methods 2015

  • Challenge 2013 focussed on 2D, low and high density

  • Super-resolution microscopy wins the 2014 Nobel Prize

  • Why Challenges?

  • 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 done be the developers themselves who participated to a challenge 2013 or to the challenge 2016.



Second edition of the challenge presented at SMLMS 2016

This edition is focussed on three 3D localization modalities: astigmatism, biplane, or double-helix. The second edition of the challenge held in the Single Molecule Localization Microscopy Symposium (SMLMS) at Lausanne, Switzerland, August 28-30, 2016.

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Special session on YouTube

In the SMLMS symposium, the special session of the Challenge will be live webcasted on a YouTube Channel, Sunday 28 August 2016, 15:00 CEST

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Super-resolution fight club

News and views of Nature Photonics: Seamus Holden and Daniel Sage Nature Photonics 10, 2016.

This edition will be focussed on both 3D localization techniques. Broad participation is warmly encouraged!

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Publication of the results in Nature Methods 2015

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 12, 717–724 (2015).

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Challenge 2013 focussed on 2D, low and high density

The Grand Challenge "Localization Microscopy" was presented as a workshop in the conference IEEE ISBI 2013 at San Francisco. Nearly 30 software have been run, mostly by the authors of the software, thus constituting the first world-wide effort in benchmarking the SMLM software. The results are published in this paper. The challenge is now re-open as a online permanent challenge.

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Super-resolution microscopy wins the 2014 Nobel Prize

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 ...

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Why Challenges?

These challenges are the first attempt to foster the community to use the same common reference datasets to evaluate the performances of the localization software.
Collaboration through competition: Nature Methods Editorial, Nature Methods 11, 695 (2014).
Grand Challenge: These SMLM challenges are part of the Grand-Challenge in Biomedical Image Analysis.


Open software initiative for bioimaging informatics

This localization microscopy challenge goes hand in hand with the Open Bio Image Alliance (OBIA) mission. This consortium for bioimaging informatics aims at providing high-quality resources to bio ...

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Update of the challenge1 Sept. 2017

Thanh-an Pham has a talk at the SMLMS 2017 Symposium in London: Developments of the ongoing 3D SMLM software challenge.

Software 11 Jul. 2017

Update of the directory of SMLM software packages. 83 SMLM software are now identified and referred.

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.

Participation1 August 2016

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

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.

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.

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