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

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

in Computer programs / Data analysis / Image resolution / Localization / Microscopy / Software / Software development / Software packages

2019

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

in Computer programs / Data analysis / Image resolution / Localization / Microscopy / Software / Software development / Software packages

2019

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

in Computer programs / Data analysis / Image resolution / Localization / Microscopy / Software / Software development / Software packages

2019

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Journal Article

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

Archetti, Anna,

Henriques, Ricardo,

Thanh-An, Pham,

Colabrese Silvia,

Jean-Baptiste, Sibarita,

Sage, Daniel,

Babcock Hazen,

Chao, Jerry,

Unser, Michael,

Velmurugan Ramraj,

Rieger Bernd,

Holden, Seamus,

Ober Raimund,

Agrawal Anurag,

Hagen, Guy M,

Lukes Tomas,

Herbert, Alex,

Ries, Jonas,

Pengo, Thomas,

Wheeler, Ann

2019

Overview

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.This study reports results from the second community-wide single-molecule localization microscopy software challenge, which tested over 30 software packages on realistic simulated data for multiple popular 3D image acquisition modes, as well as 2D localization microscopy.

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Publisher

Nature Publishing Group

Subject

/ Software development