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Super-resolution fight club: A broad assessment of 2D & 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, View ORCID ProfileSeamus Holden
doi: https://doi.org/10.1101/362517
Daniel Sage
1Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
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  • For correspondence: daniel.sage@epfl.ch seamus.holden@ncl.ac.uk
Thanh-An Pham
1Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
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Hazen Babcock
2Harvard Center for Advanced Imaging, Harvard University, Cambridge, Massachusetts, USA
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Tomas Lukes
3Laboratory of Nanoscale Biology & Laboratoire d’Optique Biomédicale, STI - IBI, EPFL, Lausanne, Switzerland
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Thomas Pengo
4University of Minnesota Informatics Institute, University of Minnesota Twin Cities, USA
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Jerry Chao
5Electrical Engineering, University of Texas Dallas, Richardson, Texas, USA
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Ramraj Velmurugan
5Electrical Engineering, University of Texas Dallas, Richardson, Texas, USA
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Alex Herbert
6MRC Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
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Anurag Agrawal
7Double Helix LLC, Boulder, Colorado, USA
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Silvia Colabrese
1Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
8Istituto Italiano di Tecnologia, Genova, Italy
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Ann Wheeler
9Edinburgh Super-Resolution Imaging Consortium, University of Edinburgh, UK
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Anna Archetti
10Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Bernd Rieger
11Department of Imaging Physics, Faculty of Applied Sciences, Delft University of Technology, The Netherlands
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Raimund Ober
5Electrical Engineering, University of Texas Dallas, Richardson, Texas, USA
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Guy M. Hagen
12UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs, Colorado, USA
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Jean-Baptiste Sibarita
13Institut Interdisciplinaire de Neurosciences, University of Bordeaux, France
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Jonas Ries
14European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Heidelberg, Germany
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Ricardo Henriques
15Quantitative Imaging and Nanobiophysics Group, MRC Laboratory for Molecular Cell Biology, University College London, UK
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Michael Unser
1Biomedical Imaging Group, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
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Seamus Holden
16Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, UK
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  • ORCID record for Seamus Holden
  • For correspondence: daniel.sage@epfl.ch seamus.holden@ncl.ac.uk
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ABSTRACT

With the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. To guide researchers on the optimal analytical software for their experiments, we have designed, in a large community effort, a competition to extensively characterise and rank these options. 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 single molecule localization microscopy software, provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions, and ultimately provides insight into the current limits of the field.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 01, 2018.
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Super-resolution fight club: A broad assessment of 2D & 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
bioRxiv 362517; doi: https://doi.org/10.1101/362517
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Super-resolution fight club: A broad assessment of 2D & 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
bioRxiv 362517; doi: https://doi.org/10.1101/362517

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