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the Single-Molecule Localization Microscopy Symposium

Single-Molecule Localization Microscopy  •  Software Benchmarking

Second edition of the challenge focussed on 3D

The challenge will be 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.

SMLMS Challenge: special session, posters, demos and awards

Live TV YouTube Channel: 28 August 2016, 15:00 CEST

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Software Density 2D AS DH BP Platform Run by Contact Affiliation Country
3D-DAOSTORMLD/HDOKOKPython/CAuthorHazen BabcockHarvardUSA
3D STORM ToolsLD/HDOKOKQt frameworkAuthorFabian HauserUniversity of Upper Austria, LinzAustria
3D-WTMLD/HDOKOKOKOKStandaloneAuthorShigeo WatanabeHamamatsu PhotonicsJapan
ADCGLD/HDOKJuliaAuthorNicholas Boyd and al.BerkeleyUSA
ALOHAHDOKMatlabAuthorJunhong Min, Kyong JinKAISTKorea
BrecsLD/HDOKOKOKn/aAuthorHervé RouaultJanelia FarmUSA
CSplineLD/HDOKOKOKPython/CAuthorHazen BabcockHarvardUSA
Easy-DHPSFLD/HDOKMatlabAuthorAlex DiezmannStanford UniversityUSA
FALCONHDOKOKMatlabAuthorJunhong MinKAISTKorea
FIRESTORMLD/HDOKMatlabAuthorThomas Von HofUlm UniversityGermany
STORMChaserLD/HDOKMatlab/C++AuthorAnna ArlettiEPFLSwitzerland
L1HLD/HDOKPython/CAuthorHazen BabcockHarvardUSA
LocalizerLDOKIgorExpertAnn WheelerUniversity of Edinburgh
MaLiangLDOKImageJAuthorWang YujieHuazhong UniversityChina
MIAToolLDOKOKOKOKMatlabAuthorRam VelmuruganTexas A&M UniversityUSA
MIATool (JAC)LDOKOKOKOKMatlabAuthorRam VelmuruganTexas A&M University
MIATool (RMS)LDOKOKOKOKMatlabAuthorRam VelmuruganTexas A&M University
mlePALMLD/HDOKOKMatlabAuthorHendrik DeschoutEPFLSwitzerland
OctaneLD/HDOKImageJExpertThomas PengoUniversity of MinnesotaUSA
PALMERHDOKImageJAuthorWang YujieHuazhong UniversityChina
PeakFit (MLEC)LD/HDOKImageJAuthorAlex HerbertUniversity of Sussex
PeakFit (LSE)LD/HDOKImageJAuthorAlex HerbertUniversity of SussexUK
PeakFit (MLE)LD/HDOKImageJAuthorAlex HerbertUniversity of Sussex
PeakSelectorLD/HDOKIDLExpertThomas PengoUniversity of MinnesotaUSA
QuickPALMLDOKOKImageJAuthorRicardo HenriquesUCLUK
RainSTORMLD/HDOKOKOKMatlabAuthorG. Tamas, J. SinkóUniversity of SzegedHungary
RapidSTORMLD/HDOKOKStandaloneExpertSeamus HoldenNewcastle UniversityUK
SFP EstimatorLD/HDOKQt C++AuthorManfred KirchgessnerUniversity of HeidelbergGermany
SMAPLD/HDOKOKOKOKMatlabAuthorJonas RiesEMBLGermany
SMAP-RMSLD/HDOKOKOKOKMatlabAuthorJonas RiesEMBL
SMfitLD/HDOKJuliaAuthorHayato IkomaStanford UniversityUSA
SMolPhotLD/HDOKOKPython/CAuthorMartti Pärs and al.University of TartuEstonia
ThunderSTORMLD/HDOKOKOKImageJAuthorMartin OvesnıCharles UniversityCzech Rep.
TVSTORMLD/HDOKOKMatlabAuthorJiaqing HuangOhio State UniversityUSA
WaveTracerLD/HDOKOKMetamorphAuthorAdel KechkaUniversité de BordeauxFrance
WTMLD/HDOKStandaloneAuthorShigeo WatanabeHamamatsu PhotonicsJapan

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).

© 2016 Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 19 Aug 2016