Single-Molecule Localization Microscopy  •  Software Benchmarking

Challenge 2D • Theoretical PSF

The Grand Challenge Localization Microscopy was presented as a Workshop in IEEE conference ISBI. Nearly 30 software have been run, mostly by the authors of the software, thus constituting the first world-wide effort in benchmarking the localization software in a comprehensive review.

The results are in the paper: Sage et al. Quantitative evaluation of software packages for SMLM, Nature Methods 12, 2015.

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Realistic Simulations • 2D • Theoretical PSF

These datasets are simulated sequence of realistic frames. The bio-inspired samples are 3D continuous models that imitates biological structures. These datasets were used for the challenge 2013.

Reference: Sage et al. Quantitative evaluation of software packages for SMLM, Nature Methods 12, 2015.

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Tubular structure • Constest datasets

Published February 1, 2013 as training dataset for the SMLM challenge 2013

1 LS
Tubulins of various diameters 10'000 frames Low density, long sequence
1 HD
Tubulins of various diameters 1'000 frames High density, short sequence
2 LS
Network of tubulins 12'000 frames Low density, long sequence
2 HD
Network of tubulins 1'200 frames High density, short sequence
3 LS
Helicoidal tubes, deep sample from 0 to 1μm 7'000 frames Low density, long sequence
3 HD
Helicoidal tubes, deep sample from 0 to 1μm 600 frames High density, short sequence

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Tubular structure • Training datasets

Published February 1, 2013 as training dataset for the SMLM challenge 2013

Two structures:

Tubulins: This sample consists to a realistic structure of 7 tubulins (constant diameter 25 nm) and 1 tubulin (constant diameter 40 nm

Bundled Tubes: Bundles of 8 tubes of 30 nm diameter2

Tubulins I
100000 fluorophores 2400 frames Low level of read-out noise 2D, theoretical PSF
Tubulins II
100000 fluorophores 2400 frames Low level of read-out noise 2D, theoretical PSF
Bundled Tubes Long Sequence
81049 fluorophores 12000 frames 2D, theoretical PSF
Bundled Tubes High Density
81049 fluorophores 168 frames 2D, theoretical PSF

Real Experiments • 2D

The experimental datasets consist of sequence of frames from real stained biologicial samples. The standard acquisition parameters are also provided.

Tubulin ConjAL647

Experimental sequence of 27'529 frames (128x128 pixels) with the parameters of acquisition.

Reference: Suliana Manley, Julia Gunzenhäuser and Nicolas Olivier, Current Opinion in Chemical Biology 15, 2011.

Tubulin AF647

The dataset represents a fixed cell, stained with mouse anti-alpha-tubulin primary antibody and Alexa647 secondary antibody. The intermittent increase in signal is due reactivation with a 405 nm laser.
This dataset is an experimental sequence of 9990 frames of 128x128 pixels.

Courtesy of Nicolas Olivier and Suliana Manley, LEB, EPFL

Tubulin • 2D • Long Sequence

Experimental sequence of 1'500 frames with the parameters of acquisition
High density of fluorophores per frame.

Courtesy of Nicolas Olivier and Debora Keller, LEB, EPFL

Tubulin • 2D • High Density

Experimental sequence of 500 frames with the parameters of acquisition
High density of fluorophores per frame.

Courtesy of Nicolas Olivier and Debora Keller, LEB, EPFL

© 2018 Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 30 Nov 2018