Single-Molecule Localization Microscopy  •  Software Benchmarking

Directory of SMLM software

This directory presents software for the single-molecule localization microscopy field. We mainly focus on the image analysis task: the accurate localization for the super-resolution reconstruction. Nevertheless, the list includes also other useful software performing deconvolution, rendering and clustering. Many of localization software have taken part to the software benchmarking: Challenge 2D or to the Challenge 3D, therefore results of localizations on common reference datasets are presented on: Results 2D and Results 3D.

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 analys...
2013
3D-DAOSTORMLocalization
Gaussian
MLE
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 localization...
2012
3D-SparseSRDeconvolution


Registered
Li Qiu Weiss
Colorado School of Mines
USA

2016
3D-STORM ToolsLocalization

Qt framework
Proprietary
Author
2016
Fabian Hauser
University of Upper Austria Linz
Austria

2016
3D-WTMLocalization
Wedge
Matching
Stand-alone
Author
2016
Shigeo Watanabe
Hamamatsu Photonics K.K.
Japan
FOM 2013
S. Watanabe et al Evaluation of Localization Algorithm of Hi...
2013
ADCGLocalization
Gaussian
ADCG
Julia
Open access
Author
2016
Nicholas Boyd
University of Berkeley
USA
SIAM Optim. 27
N. Boyd G. Schiebinger B. Recht The Alternating Descent Cond...
2017
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 using ...
2015
ANNA-PALMLocalization
Learnt
Deep neural Network
Python
Open access
Pasteur Institute ParisFrance
Nature Biotechnology
W. Ouyang Deep learning massively accelerates super-resoluti...
2018
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
Universite Grenoble-Alpes Grenoble
France
GRETSI Conf. 2015
R. Bacher F. Chatelain L. Guyon Approche bayesienne non para...
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-Feraud High density molecule...
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 M...
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 compre...
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 algorithm ...
2011
DeepLocoLocalization

Learn

OpenAccess
USA
bioRxiv
N. Boyd E. Jonas H.Babcock B: Recht DeepLoco: Fast 3D Locali...
2017
DECODELocalization
Learn
Deep neural Network
Python / Theano
Later on
Author
2016
Artur Speiser - Srinivas Turagas - Jakob Macke
Janelia Farm
USA

2018
DeconSTORMDeconvolution

Matlab
Open access
Eran Mukamel
Havard University (Zhuang group) Cambridge MA
USA
Biophysical Journal 102
E. A. Mukamel H. Babcock X. Zhuang Statistical Deconvolution...
2012
DoMLocalization
Gaussian
LS
ImageJ
Open access
Cell Biology Group - Utretch UniversityNL

2018
Easy-DHPSFLocalization
2 Gaussians
LS - Template matching for Z
Matlab
Open Access
Author
2016
Alex von Diezmann - Camille Bayas - W. E. Moerner
Stanford University Department of Chemistry Stanford
USA
Nature Protocol Exchange
M. Lew et al. Easy-DHPSF open-source software for three-dime...
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 ro...
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-SNR...
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
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 Presyna...
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 Localizatio...
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 accura...
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 Fluoroph...
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 ach...
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-time...
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 for...
2012
LEAPLocalization
Arbitrary
FIR
Python
Open access
Author
2016
Hanjie Pan
EPFL Lausanne
Swiss
Astronomy & Astrophysics 608
H. Pan M. M. J.-A. Simeoni P. Hurley T. Blu and M. Vetterli....
2017
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 Fas...
2013
LAMAClustering

Stand-alone
Open access
Sebastian Malkusch
University Frankfurt
Germany
Scientific Reports 6
S. Malkusch M. Heilemann Extracting quantitative information...
2016
LH-PALMLocalization


Registered
Chunqiang Li
Unversity of Texas El Paso
USA

2018
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 photoa...
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 and ...
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 Local...
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 likelihood ...
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 for ...
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 localizatio...
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 u...
2014
mlePALMLocalization

Matlab
Author
2016
Hendrik Deschout
Laboratory of Nanoscale Biology EPFL
Swiss

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 algor...
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 Mar...
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 F...
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 locali...
2011
PALMERLocalization

ImageJ
Open access
Author
2016
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 capable ...
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 Qu...
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
2016
USA
PNAS 9
G. Shtengel et al. Interferometric fluorescent super-resolut...
2009
PicassoLocalization

Python
Open access
Molecular Imaging and Bionanotechnology - Max Plack Institute - MunichGermany
Nature Protocols 12
J. Schnitzbauer et al. Super-resolution microscopy with DNA-...
2017
Physics-LeidenLocalization

Matlab
Registered
Rolf Harkes
Leiden University
NL

2014
pSMLM-3DLocalization

ImageJ
Open access
Author
2013
2016
Koen Martens and Johannes Hohlbein
Laboratory of Biophysics Wageningen University
NL
The Journal of Chemical Physics 148
K. Martens et al. Phasor based single-molecule localization ...
2018
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-10...
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 calcula...
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 localisatio...
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 softw...
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 im...
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 de...
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 SimpleS...
2014
SMAPLocalization
Gaussian
MLE radial symmetry
Matlab
Open access
Author
2016
Yiming Li and Jonas Ries
EMBL Heidelberg
Germany
Nature Methods 15
Yiming Li et al. Real-time 3D single-molecule localization u...
2018
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
A. Loot - A. Valdmann - M. Eltermann - M. Kree - M. Pars
University of Tartu Institute of Physics
Estonia

2016
SOLAR_STORMLocalization

L1-Homotopy
Matlab / C
Author
2016
Yoon J. Jung - Anthony Barsic - Rafael Pietsun - Nikta Fakhri
Fakri Lab MIT
USA
GPU-Accelerated Hybrid Algorithm for 3D Localization of Fluorescent Emitters in Dense Clusters
Y. Jung A. Barsic R. Piestun N. Fakhri
APS March Meeting 2017
SOSpluginLocalization
Gaussian
LS
ImageJ
Open access
Author
2013
Ihor Smal
Erasmus MC - University Medical Center Rotterdam
NL

2013
SPARCOMLocalization

Sparsity-based correlation
Matlab
Open access
Registered
Oron Solomon
Technion - Israel Institute of Technology
Israel
Optics Express 14
O. Solomon et al. Sparsity-based Super-resolution Microscopy...
2018
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 local...
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 plugi...
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 recons...
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. Sibarita Re...
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 Hi...
2013
ZOLA-3DLocalization
Learnt (Zernike coef.)
ImageJ
Open access
Registered
Benoit Lelandais
Pasteur Institute Paris
France
Nature Communication 9
A. Aristov et al. ZOLA-3D allows flexible 3D localization mi...
2018

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