Single-Molecule Localization Microscopy  •  Software Benchmarking

Collection of reference datasets

The benchmarking of SMLM software package mainly relies on the usage of common reference datasets, in particular synthetic datasets with known ground-truth.

Conditions of use These reference datasets are designed to be largely used by the developpers to validate software and by the users to check a software. Reference: Sage et al. Quantitative evaluation of software packages for SMLM, Nature Methods 12, 2015.

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Tubulin AF647

Datasets » Real Experimentation » Tubulin AF647

The dataset is a fixed cell, stained with mouse anti-alpha-tubulin primary antibody and Alexa647 secondary antibody.

File distribution

The dataset consists in 9990 frames of 128x128 pixels stored as TIFF in 16 bits.

File compression None ZIP
Unique file TubulinAF647.tif • 328.6Mb TubulinAF647.tif.zip • 210.6Mb
9990 files TubulinAF647-seq.zip • 218.5Mb

Imaging conditions

The intermittent increase in signal is due reactivation with a 405 nm laser.

  • Excitation: 635 nm
  • Objective: 100x, 1.46 NA
  • Pixel size: 100 nm
  • Number of frames: 10000 (reduced to the last 9990 frames)
  • Frame rate: 25 frames/sec

Localization and rendering in 1280x1280 pxiels

Preview Rendered image
Localization coordinates
Octane tubulin-af647/rendered-octane-256x256

Full size rendered image
(PNG image 1280x1280 pixels):

Download image


File of Localization coordinates (CSV format):

Download in the ZIP file

See the CSV text file


Settings of the algorithm:

See the screenshot

Quickpalm tubulin-af647/rendered-quickpalm-256x256

Full size rendered image
(PNG image 1280x1280 pixels):

Download image


File of Localization coordinates (CSV format):

Download in the ZIP file

See the CSV text file


Settings of the algorithm:

See the screenshot

Rapidstorm tubulin-af647/rendered-rapidstorm-256x256

Full size rendered image
(PNG image 1280x1280 pixels):

Download image


File of Localization coordinates (CSV format):

Download in the ZIP file

See the CSV text file


Settings of the algorithm:

See the screenshot

Crop of resulting image
(256x256 pixels)

Rendered image by the
software Octane Rendered image by the
software QuickPALM

tubulin-af647/mip
Maximum intensity time-projection

tubulin-af647/stdev
Standard deviation time-projection

© 2017 Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 31 Mar 2017