Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

Daniel Sage; Thanh-An Pham; Hazen Babcock; Tomas Lukes; Thomas Pengo; Jerry Chao; Ramraj Velmurugan; Alex Herbert; Anurag Agrawal; Silvia Colabrese; Ann Wheeler; Anna Archetti; Bernd Rieger; Raimund Ober; Guy M Hagen; Jean-Baptiste Sibarita; Jonas Ries; Ricardo Henriques; Michael Unser; Seamus Holden

doi:10.1038/s41592-019-0364-4

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

Nat Methods. 2019 May;16(5):387-395. doi: 10.1038/s41592-019-0364-4. Epub 2019 Apr 8.

Authors

Daniel Sage^#¹, Thanh-An Pham^#², Hazen Babcock³, Tomas Lukes^{4

5}, Thomas Pengo⁶, Jerry Chao^{7

8}, Ramraj Velmurugan^{8

9}, Alex Herbert¹⁰, Anurag Agrawal¹¹, Silvia Colabrese^{2

12}, Ann Wheeler¹³, Anna Archetti¹⁴, Bernd Rieger¹⁵, Raimund Ober^{7

8

16}, Guy M Hagen¹⁷, Jean-Baptiste Sibarita^{18

19}, Jonas Ries²⁰, Ricardo Henriques²¹, Michael Unser², Seamus Holden^#²²

Affiliations

¹ Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. [email protected].
² Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
³ Harvard Center for Advanced Imaging, Harvard University, Cambridge, MA, USA.
⁴ Laboratory of Nanoscale Biology and Laboratoire d'Optique Biomédicale, STI - IBI, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
⁵ Department of Radioelectronics, FEE, Czech Technical University, Prague, Czech Republic.
⁶ University of Minnesota Informatics Institute, University of Minnesota Twin Cities, Minneapolis, MN, USA.
⁷ Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.
⁸ Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX, USA.
⁹ Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, USA.
¹⁰ MRC Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
¹¹ Double Helix LLC, Boulder, CO, USA.
¹² Istituto Italiano di Tecnologia, Genova, Italy.
¹³ Advanced Imaging Resource, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
¹⁴ Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
¹⁵ Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands.
¹⁶ Centre for Cancer Immunology, University of Southampton, Southampton, UK.
¹⁷ UCCS Center for the Biofrontiers Institute, University of Colorado, Colorado Springs, CO, USA.
¹⁸ Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France.
¹⁹ Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique (CNRS) UMR 5297, Bordeaux, France.
²⁰ European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany.
²¹ Quantitative Imaging and Nanobiophysics Group, MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
²² Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK. [email protected].

^# Contributed equally.

Abstract

With the widespread uptake of two-dimensional (2D) and three-dimensional (3D) single-molecule localization microscopy (SMLM), a large set of different data analysis packages have been developed to generate super-resolution images. In a large community effort, we designed a competition to extensively characterize and rank the performance of 2D and 3D SMLM software packages. We generated realistic simulated datasets for popular imaging modalities-2D, astigmatic 3D, biplane 3D and double-helix 3D-and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D SMLM software and provides a holistic view of how the latest 2D and 3D SMLM packages perform in realistic conditions. This resource allows researchers to identify optimal analytical software for their experiments, allows 3D SMLM software developers to benchmark new software against the current state of the art, and provides insight into the current limits of the field.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Image Processing, Computer-Assisted / methods*
Imaging, Three-Dimensional / methods*
Single Molecule Imaging / methods*
Software*

Abstract

Publication types

MeSH terms

Grants and funding