Real datasets 2D

Realistic Simulations 2D

Datasets of the Challenge 2013

The benchmarking of SMLM software package mainly relies on the usage of common reference datasets. This page contains a collection of localization microscopy simulated datasets that were used to conduct the challenge 2013. They are generated with a 2D theoretical PSF.

This page contains Contest Datasets used to assess software package, Training Datasets which are provided with ground-truth localizations, and Artifical Constructions which are toy examples.

Reference: Sage et al., Quantitative Evaluation of Software Packages for Single-Molecule Localization Microscopy Open-access PDF, Nature Methods 2019.

Contest Datasets

Long Sequence
Three datasets of network of tubulins, ~10'000 frames, low denstiy of emitters

1_LS 2_LS 3_LS
2D PSF, noisy and autofluorescence background.

High Density
Three datasets of network of tubulins, ~700 frames, high denstiy of emitters

1_HD 2_HD 3_HD
2D PSF, noisy and autofluorescence background.

Training Datasets (with Ground-truth Localizations)

This sample consists to a realistic structure of 7 tubulins (constant diameter 25 nm) and 1 tubulin (constant diameter 40 nm). The depth of the sample is from 0 to 300 nm. 100000 fluorophores are activated over 2400 frames.

Tubulins_I
Low level of read-out noise autofluorescence background.

Tubulins_II
High level of read-out noise and autofluorescence background.

Bundles of 8 tubes of 30 nm diameter

Bundled Tubes High Density
High-density, 81'049 fluorophores on 168 frames

Bundled Tubes Long Sequence
Sparse density, 81'049 molecules on 12'000 frames

Artificial Constructions (Toy Examples)

These datasets represents artificial structure with some actived fluorophores at some specific postions. These datasets are mainly used to evaluated particular features of the localization software, like the ability to discriminate two neighboring fluorophores in the same frame.

Dataset Eye
This dataset consists to 4 non-overlapping tubes of 1nm of radius in a field of view 38.4 x 38.4 μm. Only 300 fluorophores are activated in 40 frames. It is an ideal dataset: no perturbation, no additional noise.

Dataset Snow
This dataset contains fluorophores are placed on a regular grid with various depth and various number of photons. The field of view is 50 μm x 50 μm.

Dataset Seashell
The synthetic sample has been created articifically using a 3D artificial structure shape. This shape represents a seashell of six branches with various fluorophore densities. This sample is provided in two versions: flat sample (no Z) and thick sample (1 μm of depth).