Single-Molecule Localization Microscopy  •  Software Benchmarking

Second edition of the challenge focussed on 3D

The challenge has been presented at Single Molecule Localization Microscopy Symposium (SMLMS) at Lausanne, Switzerland, August 28-30, 2016. This edition will be focussed on 3D localization techniques, astigmatism, biplane, or double-helix.


Get involved!

Pre-registration gives access to the ground-truth of the training datasets and to the frames sequence of the contest datasets. The challenge is open to all individuals or teams, academic or corporate, existing or newly developed localization microscopy software. Participation is free.

How to register? To announce your participation, send an email to indicating the name of the software that you want to represent and the name of a contact person.

How to participate?

  • Pre-register by send an email with the name of the software and a contact name
  • Choose one or several modalities: 2D, AS (3D-astigmatism), DH (3D-double-helix) or BP (3D-biplane)
  • Download the datasets and the z-stack of beads for your calibration.
  • Submit your documents
  • Optionally, you are encourage to attend to the SMLMS conference

Documents to submit

  • 3 questionnaires, general information, usability, and computational time
  • 1 wobble correction process: localization on the z-stack of beads, wooble correction file, or localization already corrected by the software
  • 4 localization files of a given category/modality
    • File format: the results of the localization are given in a delimiter-separated values text file, typically in a coma-separated values (CSV) or tab-separated values (TSV/TAB). The unreadable lines are discarded (e.g. NaN).
    • At least the following columns: X, Y, Z, frame, number of photons. The organizers reserve the right to permute the columns.
    • To better fit the same origin, the organizers reserve the right to apply the following offset: -50nm on X (1/2 pixel), -50nm on Y (1/2 pixel), -750 nm (focal plane at 750nm), +1 frame (index of first frame is 1).

Challenge discussion forum

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