Benchmarking of SMLM Software
Comprehensive review of the single-molecule localization microscopy (SMLM, PALM, STORM) software packages.
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  and was was recognized with the 2014 Nobel Prize in chemistry . 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.
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  and a challenging task , as the data is very long image sequence.
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