Single-Molecule Localization Microscopy  •  Software Benchmarking

Directory of SMLM software

This directory presents to image reconstruction software for the single-molecule localization microscopy field. We mainly focus on the main task: the accurate localization task. In addition, we present other software that perform deconvolution, rendering and clustering. Many of these software have taken part to the software benchmarking: Challenge 2013 or to the Challenge 2016, therefore results of localizations on common reference datasets are presented on: Results Challenge 2013 and Results Challenge 2016.

We are trying to maintain up to date this list of software. In case of inexact or missing information, please contact us.

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Software Main Task Open Access Challenge Contact Ctry Reference Year
3BDeconvolution

ImageJ
Open access
Randall Division of Cell and Molecular Biophysics at the Kings College, LondonUK
Nature Methods 10
E. Rosten,G. Jones, S. Cox, ImageJ plug-in for Bayesian anal...
2013
3D-DAOSTORMLocalization
Gaussian
LS-DAOPHOT
Python / C
Open access
Author
2013
2016
Hazen Babcock
Harvard University (Zhuang group), Cambridge, MA
USA
Optical Nanoscopy 1
H. Babcock, Y. Sigal, X. Zhuang, A high-density 3D localizat...
2012
3D-STORM ToolsLocalization

Qt framework
Proprietary
Fabian Hauser
University of Upper Austria, Linz
Austria

2016
3D-WTMLocalization
Wedge
Matching
Stand-alone
Shigeo Watanabe
Hamamatsu Photonics K.K.
Japan
FOM 2013
S. Watanabe et al, Evaluation of Localization Algorithm of H...
2013
ADCGLocalization
Gaussian
ADCG
Julia
Open access
Author
2016
Nicholas Boyd
University of Berkeley
USA
arXiv
N. Boyd, G. Schiebinger, B. Recht, The Alternating Descent C...
2015
a-livePALMLocalization
Gaussian
MLE
Matlab
Access on request
Author
2013
Yiming Li
Institute of Applied Physics Karlsruhe Institute of Technology (KIT) Karlsruhe
Germany
ACS Nano 7
Y. Li et al. Fast and efficient molecule detection in locali...
2013
ALOHADeconvolution

Matlab
Author
2016
Junhong Min and Kyong Jin
Bio-Imaging and Signal Processing Lab, KAIST
Korea
SPIE Optical Engineering 9597
Min, Junhong, Fast live cell imaging at nanometer scale usin...
2015
Auto-BayesLocalization
Gaussian, Weibull
LS
Stand-alone
Open access
Author
2013
Yunqing Tang and Luru Dai
National Center for Nanoscience and Technology, Beijing
China

2015
B-recsLocalization
Arbitrary
MMSE, MAP
C / ImageJ
Open access
Author
2013
2016
Herve Rouault
Janelia Farm Research Campus, HHMI
USA

2013
BacherLocalization


Registered
Raphael Bacher
Université Grenoble-Alpes, Grenoble
France
GRETSI Conf. 2015
R. Bacher, F. Chatelain, L. Guyon, Approche bayésienne non ...
2015
C2SILocalization


Registered
Oron Solomon
Technion - Israel Institute of Technology
Israel

2015
CEL0-STORMLocalization
Arbitrary
l0 optimization
Matlab
Later
Author
2016
Emmanuel Soubies
INRIA Sophia Antipolis
France
IEEE ISBI 2017
S. Gazagnes, E. Soubies, L. Blanc-Féraud, High density mole...
2017
ClearPALMLocalization

Matlab
Registered
Arun Shivanandan
Laboratory of Nanoscale Biology, EPFL
Swiss

2007
CodeBlocksLocalization


Registered
David Thomas Price
University of Arizona
USA

2013
Compressing Sessing STORMLocalization


Registered
Sebastion Deppendorf
Bielefeld University
Germany

2016
Convolutional-Moment-PursuitLocalization


Registered
Gergo Bohner
University College London
UK

2015
CsplineLocalization
Cubic spline model
MLE
Python / C
Open access
Author
2016
Hazen Babcock
Harvard University (Zhuang group), Cambridge, MA
USA
Scientific Reports 7
H. Babcok, X. Zhuang, Analyzing Single Molecule Localization...
2017
CSSTORM FasterSTORMDeconvolution
Gaussian
Compressed sensing
Matlab
Open access
Expert
2013
Department of Earth and Environment, Florida International University, MiamiUSA
Nature Methods 9
L. Zhu, W. Zhang, D. Elnatan, B. Huang, FasterSTORM using co...
2012
DAOSTORMLocalization
Measured
LS-DAOPHOT
Python
Open access
Author
2013
Seamus Holden
Laboratory of Experimental Biophysics, EPFL
UK
Nature Methods 8
S.J. Holden, S. Uphoff, A.N. Kapanidis, DAOSTORM: an algorit...
2011
DeepSTORMLocalization


Registered
Artur Speiser
Neural System Analysis, Caesar, Bonn
Germany

2017
DeconSTORMDeconvolution

Matlab
Open access
Eran Mukamel
Havard University (Zhuang group), Cambridge, MA
USA
Biophysical Journal 102
E. A. Mukamel, H. Babcock, X. Zhuang, Statistical Deconvolut...
2012
Easy-DHPSFLocalization
2 Gaussians
LS - Template matching for Z
Matlab
Open Access
Author
2016
Alex von Diezmann, Camille Bayas, and W. E. Moerner
Stanford University Department of Chemistry, Stanford
USA
Nature Protocol Exchange
M. Lew et al., Easy-DHPSF open-source software for three-dim...
2013
EMLocalization


Yi Sun
Department of Electrical Engineering, The City College of City University of New York
USA

2016
FacePALMDeconvolution
Arbitrary
Python
Author
Eelco Hoogendoorn
Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam
NL
FOM 2013
E. Hoogendoorn et al., Image deconvolution techniques with r...
2013
FALCONLocalization
Taylor Approximation
ADMM
Matlab
Open access
Author
2013
2016
Junhong Min and Jong Chul Ye
Bio-Imaging and Signal Processing Lab, KAIST
Korea
Scientific Reports 4
Junhong Min et al., FALCON: fast and unbiased reconstruction...
2014
Fast-ML-HDLocalization
Gaussian
MLE
Matlab
Author
2013
Kyungsang Kim and Jong Chul Ye
Bio-Imaging and Signal Processing Lab, KAIST
Korea
SampTA Conf. 2013
K.S. Kim et al., Fast maximum likelihood high-density low-SN...
2013
FastSRLocalization


Registered
Yanhua Wang and Leslie Ying
Department of Biomedical Engineering and Department of Electrical Engineering, University at Buffalo
USA

2013
FIRESTORMLocalization
Gaussian
LS
Matlab
Access on request
Author
2016
Thomas Vomhof and Jochen Reichel
Institute of Biophysics, Ulm University
Germany
Front. Cell. Neurosciences 9
M. Schoen et al., Super-Resolution Microscopy Reveals Presyn...
2016
FOCALClustering

Matlab
Open access
Department of Physics, University of Toronto, TorontoCanada
Bioinformatics 32
A. Mazouchi J. N. Milstein, Fast Optimized Cluster Algorithm...
2016
SFP Estimator (FGPA)Localization
Gaussian
MLE, Center of mass
Stand-alone (QT C++)
Open-access
Author
2013
2016
Manfred Kirchgessner and Frederik Gruell
Heidelberg University
Germany
Int. Conf. FPL 2011
F. Gruell et al., Accelerating Image Analysis for Localizati...
2011
Gauss2dcircLocalization
Gaussian
Regression
Matlab
Open access
Author
2013
Stephen Anthony
University of Illinois, Urbana, Illinois
USA
Langmuir 25
S.M. Anthony, S. Granick, Image analysis with rapid and accu...
2009
GMIMPROLocalization

ImageJ
Open access
Division of Physical Biochemistry, MRC National Institute for Medical Research, LondonUK
Biophysical Journal 92
G. Mashanov, J. Molloy, Automatic Detection of Single Fluoro...
2007
GPUgaussMLE gaussMLEv2Localization
Gaussian
MLE
Matlab
Open access
Author
2013
Keith Lidke and Bernd Rieger
Delft University of Technology
NL
Nature Methods 7
C.S. Smith et al., Fast, single-molecule localization that a...
2010
GR-IMLLocalization


Marco Castello and Francesca Pennacchietti
Istituto Italiano di Tecnologia
Italy

2014
GraspJLocalization
Gaussian
MLE
ImageJ
Open access
Author
2013
Norman Brede and Melike Lakadamyali,
ICFO-Institut de Ciencies Fotoniques, Barcelona
Spain
Optical Nanoscopy 1
N. Brede and M. Lakadamyali, GraspJ: an open source, real-ti...
2012
iNMFDeconvolution

Matlab
Open access
Ondrej Mandula
Fondation Nanosciences, Grenoble
France
Optics express 22.20
O. Mandula et al., Localisation microscopy with quantum dots...
2014
Insight3Localization
Arbitrary
LS
Stand-alone
Commercial
Author
2013
Ryan McGorty and Bo Huang
Dept of Pharmaceutical Chemistry, University of California, San Francisco
USA

2013
JD LocalizationLocalization

Matlab
Open access
Josh Larkin
University of Oxford, Oxford
UK
Optics Express 20
J. Larkin, P. Cook, Maximum precision closed-form solution f...
2012
L1HLocalization
Gaussian, Arbitrary
L1-Homotopy
Python
Open access
Author
2013
2016
Hazen Babcock
Harvard University, Cambridge, MA
USA
Optics Express 21
Hazen Babcock, Jeff Moffit, Yunlong Cao and Xiaowei Zhuang, ...
2013
LAMAClustering

Stand-alone
Open access
Sebastian Malkusch
University Frankfurt
Germany
Scientific Reports 6
S. Malkusch, M. Heilemann, Extracting quantitative informati...
2016
livePALM2Localization

Matlab
Access on request
Registered
Yiming Li
Institute of Applied Physics Karlsruhe Institute of Technology (KIT) Karlsruhe
Germany
Nature Methods 6
P. N. Hedde et al., Online image analysis software for photo...
2009
LocalizerLocalization

Igor
Open access
Expert
2016
Department of Chemistry, University of LeuvenBelgium
J. of Biomedical Optics 17
P. Dedecker et al., Localizer: fast, accurate, open-source, ...
2012
Loco_PALMLocalization


Registered
Johannes Hohlbein
Wageningen University & Research
NL

2015
Lucky ImagingLocalization
Lucky Image
Gaussian

Brid Cronin
Keble College, Oxford
UK
Biophysical Journal 96
B. Cronin, B. de Wet, M. Wallace, Lucky Imaging: Improved Lo...
2009
M2LELocalization
Gaussian
MLE
ImageJ
Open access
Author
2013
Shane Stahlheber and Alex Small
California State Polytechnic University, Pomona
USA
Optics Letters 37
R. Starr, S. Stahlheber and A. Small, Fast maximum likelihoo...
2012
Matlab scriptsLocalization

Matlab
Registered
Sheng Liu
New York University
USA

2017
MaLiangLocalization
Gaussian
MLE
ImageJ
Open access
Author
2013
2016
Zhen-li Huang and Yujie Wang
Wuhan Laboratory for Optoelectronics, HUST, Wuhan
China
Optics Express 11
T. Quan et al., Ultra-fast, high-precision image analysis fo...
2010
MIAToolLocalization

Java
Open access
Author
2016
R. Velmurugan, A. V. Abraham, and R. J. Ober
Texas A&M University, College Station, Texas
USA
Optics Express, 23
A. Tahmasbi, E.S. Ward, R.J. Ober, Determination of localiza...
2015
MicroManager LMLocalization
Gaussian
LS
ImageJ
Open access
Author
2013
Nico Stuurman
Vale Lab, University of California, San Francisco
USA
J. of Biological Methods 1
A. Edelstein et al., Advanced methods of microscope control ...
2014
mlePALMLocalization

Matlab
Autthor
2016
Laboratory of Nanoscale Biology, EPFLSwiss

2016
MrSELocalization
Radial
Center of symetry
Stand-alone
Open access
Author
2013
Zhen-li Huang and Yi-na Wang
Wuhan Laboratory for Optoelectronics, HUST, Wuhan
China
Optics Letters 37
H. Ma, F. Long, S. Zeng, and Z.-L. Huang, Fast and precise a...
2012
MTTLocalization

Matlab
Access on request
Centre d'Immunologie de Marseille-Luminy and Institut Fresnel, MarseilleFrance
Nature Protocol Exchange
Arnauld Serge, Nicolas Bertaux, Herve Rigneault and Didier M...
2008
OctaneLocalization
Gaussian
LS
ImageJ
Open access
Expert
2013
2016
University of Connecticut Health CenterUSA
Biophysical Journal 4
Lili Niu and Ji Yu, Investigating intracellular dynamics of ...
2008
palm3dLocalization

Python
Open access
National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MDUSA
Nature Methods 8
A. York et al., Confined activation and subdiffractive local...
2011
PALMERLocalization

ImageJ
Open access
Zhen-li Huang and Yi-na Wang
Wuhan Laboratory for Optoelectronics, HUST, Wuhan
China
Optics Express 14
Y. Wang, T. Quan, S. Zeng, Z.L. Huang, PALMER: a method capa...
2012
PC-PALMLocalization

Matlab
The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MarylandUSA
Nature Protocol Exchange 8
P. Prabuddha, T. Jovanovic-Talisman, J. Lippincott-Schwartz,...
2013
PeakFitLocalization
Gaussian
LS
ImageJ
Open access
Author
2013
2016
Alex Herbert
Genome Damage and Stability Centre, University of Sussex
UK

2013
PeakSelectorLocalization
Gaussian
LS
IDL
Expert
2013
USA
PNAS 9
G. Shtengel et al., Interferometric fluorescent super-resolu...
2009
Physics-LeidenLocalization

Matlab
Registered
Rolf Harkes
Leiden University
NL

2014
PYMELocalization
Arbitrary
LS
Python
Open access
Author
2013
David Baddeley
Nanobiology Institute, Yale University, West Haven, USA and University of Auckland, Auckland
NZ
Nano Research 4
D. Baddeley, M.B. Cannell, C. Soeller, Three-dimensional sub...
2011
QC-STORMLocalization
Gaussian
MLE
ImageJ
Later
Author
2016
Luchang Li
Wuhan National Laboratory
China

2017
QuickPALMLocalization
Gaussian
Center of mass
ImageJ
Open access
Author
2013
2016
Ricardo Henriques
Institut Pasteur, Paris
France
Nature Methods 7
R. Henriques et al., QuickPALM: 3D real-time photoactivation...
2010
RadialSymmetryLocalization
Radial
Center of symetry
Matlab
Open access
Author
Raghuveer Parthasarathy
Department of Physics, The University of Oregon
USA
Nature Methods 9
R. Parthasarathy, Rapid, accurate particle tracking by calcu...
2012
RainSTORMLocalization

Matlab
Open access
Author
2016
G. Tamas and J. Sinko
University of Cambridge UK & University of Szeged
Hungary
Journal of Optics 15
E.J. Rees et al., Elements of image processing in localisati...
2013
RapidSTORMLocalization
Gaussian
LS, MLE
Stand-alone
Open access
Author
2013
2016
Steve Wolter, Markus Sauer
Biotechnologie and Biophysik, University of Wurzburg
Germany
Nature Methods 9
S. Wolter et al., rapidSTORM: accurate, fast open-source sof...
2012
RmDLocalization


Registered
Mo Chen and Xiaolin Nan
Oregon Health & Science University
USA

2015
SharpViSuClustering

Matlab
Open access
L. Andronov
Centre for Integrative Biology, University of Strasbourg
France
Bioinformatics 32
L. Andronov, SharpViSu: integrated analysis and segmentation...
2016
SHRImPLocalization


Department of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, ILUSA
PNAS 101
M. Gordon, T. Ha, P. Selvin, Single-molecule high-resolution...
2004
SimplePALMLocalization

Mean-shift
Stand-alone
Author
2013
Jerome Boulanger and Leila Muresan
Institut Curie, Paris, and Centre de genetique moleculaire, Gif-sur-Yvette
France
IEEE Trans. on Medical Imaging 29
J. Boulanger and al., Patch-based non-local functional for d...
2010
SimpleSTORMLocalization
Gaussian, measured
Interpolation
Python
Open access
Author
2013
Ullrich Koethe and Luca Fiaschi
Heidelberg Collaboratory for Image Processing
Germany
Histochemistry and Cell Biology 141
U. Koethe, F. Herrmannsdoerfer, I. Kats, F.A. Hamprecht, Sim...
2014
SMAPLocalization
Gaussian
MLE, radial symmetry
Matlab
Author
2016
Jonas Ries
EMBL, Heidelberg
Germany

2016
SMfitLocalization
Integrated Gaussian
ADCG
Julia / Python
Author
2016
Hayato Ikoma
Electrical Engineering Department, Stanford University
USA

2016
SNSMILLocalization
Gaussian
LS
Stand-alone
Open access
Author
2013
Yunqing Tang and Luru Dai
Chongqing University, Chongqing and National Center for Nanoscience and Technology, Beijing
China

2013
SMolPhotLocalization
Gaussian
LS
Python / C
Open access
Author
2016
Martti Pars and Ardi Loot
University of Tartu, Institute of Physics
Estonia

2016
SOLAR_STORMLocalization

L1-Homotopy
Matlab / C
Author
2016
Yoon J. Jung and Nikta Fakhri
Fakri Lab, MIT
USA

2016
SOSpluginLocalization
Gaussian
LS
ImageJ
Open access
Author
2013
Ihor Smal
Erasmus MC - University Medical Center Rotterdam
NL

2013
SparseFMMLocalization


Registered
Haowen Zhang
Tsinghua University
China

2015
SparseSRLocalization


Gongguo Tong
University of Wisconsin, Madison
USA

2013
SR-TesselerClustering

Stand-alone
Open access
University of Bordeaux and Interdisciplinary Institute for NeuroscienceFrance
Nature Methods 12
F. Levet, SR-Tesseler: a method to segment and quantify loca...
2016
STORMChaserLocalization

Matlab
Author
2016
Anna Archetti
Institute of Physics, EPFL
Swiss

2016
ThunderSTORMLocalization
Gaussian, Integrated Gaussian, Radial
LS, MLE
ImageJ
Open access
Author
2013
2016
Martin Ovesny, Guy Hagen and Pavel Krizek
Charles University, Prague
Czech
Bioinformatics 30
M. Ovesny and al., ThunderSTORM: a comprehensive ImageJ plug...
2014
TVSTORMLocalization
Gaussian
MLE, backtracking line search
Matlab
Author
2016
Jiaqing Huang
The Ohio State University, Columbus, OH
USA
IEEE ISBI 2016
J. Huang, S. Mingzhai, C. Yuejie, Super-resolution image rec...
2016
Wavelet FluoroBancroftLocalization
Gaussian
Bancroft algorithm
Matlab
Access on request
Author
2013
Sean Andersson and, Trevor Ashley
Boston University
USA
Optics Express 16
S.B. Andersson, Localization of a fluorescent source without...
2008
WaveTracerLocalization
Gaussian
LS
Metamorph
Commercial
Author
2013
2016
Adel Kechkar and Jean-Baptiste Sibarita
University of Bordeaux and Institute for Neuroscience
France
PLoS One 8
A. Kechkar, D. Nair, M. Heilemann, D. Choquet, J.-B. Sibarit...
2013
WTMLocalization
Wedge
Matching
Stand-alone
Author
2013
2016
Shigeo Watanabe
Hamamatsu Photonics K.K.
Japan
FOM 2013
S. Watanabe et al, Evaluation of Localization Algorithm of H...
2013

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