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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Software Platform Open Access PSF Fit Methods Run by Contact Year
3D-DAOSTORMPython / COpen accessGaussianMLEAuthorHazen Babcock
Harvard University (Zhuang group) Cambridge MA, USA
2012
a-livePALMMatlabAccess on requestGaussianMLEAuthorYiming Li
Institute of Applied Physics Karlsruhe Institute of Technology (KIT) Karlsruhe, Germany
2013
Auto-BayesStand-aloneOpen accessGaussian WeibullLSAuthorYunqing Tang and Luru Dai
National Center for Nanoscience and Technology Beijing, China
2015
B-recsC / ImageJOpen accessArbitraryMMSE MAPAuthorHerve Rouault
Janelia Farm Research Campus HHMI, USA
2013
CSSTORM FasterSTORMMatlabOpen accessGaussianCompressed sensingExpertDepartment of Earth and Environment Florida International University Miami, USA2012
DAOSTORMPythonOpen accessMeasuredLS-DAOPHOTAuthorSeamus Holden
Laboratory of Experimental Biophysics EPFL, UK
2011
FALCONMatlabOpen accessTaylor ApproximationADMMAuthorJunhong Min and Jong Chul Ye
Bio-Imaging and Signal Processing Lab KAIST, Korea
2014
Fast-ML-HDMatlabGaussianMLEAuthorKyungsang Kim and Jong Chul Ye
Bio-Imaging and Signal Processing Lab KAIST, Korea
2013
SFP Estimator (FGPA)Stand-alone (QT C++)Open-accessGaussianMLE Center of massAuthorManfred Kirchgessner and Frederik Gruell
Heidelberg University, Germany
2011
Gauss2dcircMatlabOpen accessGaussianRegressionAuthorStephen Anthony
University of Illinois Urbana Illinois, USA
2009
GPUgaussMLE gaussMLEv2MatlabOpen accessGaussianMLEAuthorKeith Lidke and Bernd Rieger
Delft University of Technology, NL
2010
GraspJImageJOpen accessGaussianMLEAuthorNorman Brede and Melike Lakadamyali
ICFO-Institut de Ciencies Fotoniques Barcelona, Spain
2012
Insight3Stand-aloneCommercialArbitraryLSAuthorRyan McGorty and Bo Huang
Dept of Pharmaceutical Chemistry University of California San Francisco, USA
2013
L1HPythonOpen accessGaussian ArbitraryL1-HomotopyAuthorHazen Babcock
Harvard University Cambridge MA, USA
2013
M2LEImageJOpen accessGaussianMLEAuthorShane Stahlheber and Alex Small
California State Polytechnic University Pomona, USA
2012
MaLiangImageJOpen accessGaussianMLEAuthorZhen-li Huang and Yujie Wang
Wuhan Laboratory for Optoelectronics HUST Wuhan, China
2010
MicroManager LMImageJOpen accessGaussianLSAuthorNico Stuurman
Vale Lab University of California San Francisco, USA
2014
MrSEStand-aloneOpen accessRadialCenter of symetryAuthorZhen-li Huang and Yi-na Wang
Wuhan Laboratory for Optoelectronics HUST Wuhan, China
2012
OctaneImageJOpen accessGaussianLSExpertUniversity of Connecticut Health Center, USA2008
PeakFitImageJOpen accessGaussianLSAuthorAlex Herbert
Genome Damage and Stability Centre University of Sussex, UK
2013
PeakSelectorIDLGaussianLSExpert2009
pSMLM-3DImageJOpen accessAuthorKoen Martens and Johannes Hohlbein
Laboratory of Biophysics Wageningen University, NL
2018
PYMEPythonOpen accessArbitraryLSAuthorDavid Baddeley
Nanobiology Institute Yale University West Haven USA and University of Auckland Auckland, NZ
2011
QuickPALMImageJOpen accessGaussianCenter of massAuthorRicardo Henriques
Institut Pasteur Paris, France
2010
RapidSTORMStand-aloneOpen accessGaussianLS MLEAuthorSteve Wolter Markus Sauer
Biotechnologie and Biophysik University of Wurzburg, Germany
2012
SimplePALMStand-aloneMean-shiftAuthorJerome Boulanger and Leila Muresan
Institut Curie Paris and Centre de genetique moleculaire Gif-sur-Yvette, France
2010
SimpleSTORMPythonOpen accessGaussian measuredInterpolationAuthorUllrich Koethe and Luca Fiaschi
Heidelberg Collaboratory for Image Processing, Germany
2014
SNSMILStand-aloneOpen accessGaussianLSAuthorYunqing Tang and Luru Dai
Chongqing University Chongqing and National Center for Nanoscience and Technology Beijing, China
2013
SOSpluginImageJOpen accessGaussianLSAuthorIhor Smal
Erasmus MC - University Medical Center Rotterdam, NL
2013
ThunderSTORMImageJOpen accessGaussian Integrated Gaussian RadialLS MLEAuthorMartin Ovesny Guy Hagen and Pavel Krizek
Charles University Prague, Czech
2014
Wavelet FluoroBancroftMatlabAccess on requestGaussianBancroft algorithmAuthorSean Andersson and Trevor Ashley
Boston University, USA
2008
WaveTracerMetamorphCommercialGaussianLSAuthorAdel Kechkar and Jean-Baptiste Sibarita
University of Bordeaux and Institute for Neuroscience, France
2013
WTMStand-aloneWedgeMatchingAuthorShigeo Watanabe
Hamamatsu Photonics K.K., Japan
2013

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