Directory of SMLM softwareThis 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 |
|---|---|---|---|---|---|---|---|
| 3B | Deconvolution | ImageJ Open access | Randall Division of Cell and Molecular Biophysics at the Kings College London | UK | Nature Methods 10 E. Rosten G. Jones S. Cox ImageJ plug-in for Bayesian analys... | 2013 | |
| 3D-DAOSTORM | Localization 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-SparseSR | Deconvolution | Registered | Li Qiu Weiss Colorado School of Mines | USA | 2016 | ||
| 3D-STORM Tools | Localization | Qt framework Proprietary | Author 2016 | Fabian Hauser University of Upper Austria Linz | Austria | 2016 | |
| 3D-WTM | Localization 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 |
| ADCG | Localization 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-livePALM | Localization 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 |
| ALOHA | Deconvolution | 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-PALM | Localization Learnt Deep neural Network | Python Open access | Pasteur Institute Paris | France | Nature Biotechnology W. Ouyang Deep learning massively accelerates super-resoluti... | 2018 | |
| Auto-Bayes | Localization Gaussian Weibull LS | Stand-alone Open access | Author 2013 | Yunqing Tang and Luru Dai National Center for Nanoscience and Technology Beijing | China | 2015 | |
| B-recs | Localization Arbitrary MMSE MAP | C / ImageJ Open access | Author 2013 2016 | Herve Rouault Janelia Farm Research Campus HHMI | USA | 2013 | |
| Bacher | Localization | Registered | Raphael Bacher Universite Grenoble-Alpes Grenoble | France | GRETSI Conf. 2015 R. Bacher F. Chatelain L. Guyon Approche bayesienne non para... | 2015 | |
| CEL0-STORM | Localization 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 |
| ClearPALM | Localization | Matlab | Registered | Arun Shivanandan Laboratory of Nanoscale Biology EPFL | Swiss | 2007 | |
| CodeBlocks | Localization | Registered | David Thomas Price University of Arizona | USA | 2013 | ||
| Compressing Sessing STORM | Localization | Registered | Sebastion Deppendorf Bielefeld University | Germany | 2016 | ||
| Convolutional-Moment-Pursuit | Localization | Registered | Gergo Bohner University College London | UK | 2015 | ||
| Cspline | Localization 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 FasterSTORM | Deconvolution Gaussian Compressed sensing | Matlab Open access | Expert 2013 | Department of Earth and Environment Florida International University Miami | USA | Nature Methods 9 L. Zhu W. Zhang D. Elnatan B. Huang FasterSTORM using compre... | 2012 |
| DAOSTORM | Localization 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 |
| DeepLoco | Localization Learn | OpenAccess | USA | bioRxiv N. Boyd E. Jonas H.Babcock B: Recht DeepLoco: Fast 3D Locali... | 2017 | ||
| DECODE | Localization Learn Deep neural Network | Python / Theano Later on | Author 2016 | Artur Speiser - Srinivas Turagas - Jakob Macke Janelia Farm | USA | 2018 | |
| DeconSTORM | Deconvolution | 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 | |
| DoM | Localization Gaussian LS | ImageJ Open access | Cell Biology Group - Utretch University | NL | 2018 | ||
| Easy-DHPSF | Localization 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 |
| EM | Localization | Yi Sun Department of Electrical Engineering The City College of City University of New York | USA | 2016 | |||
| FacePALM | Deconvolution 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 |
| FALCON | Localization 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-HD | Localization 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 |
| FastSR | Localization | Registered | Yanhua Wang and Leslie Ying Department of Biomedical Engineering and Department of Electrical Engineering University at Buffalo | USA | 2013 | ||
| FIRESTORM | Localization 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 |
| FOCAL | Clustering | Matlab Open access | Department of Physics University of Toronto Toronto | Canada | 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 |
| Gauss2dcirc | Localization 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 |
| GMIMPRO | Localization | ImageJ Open access | Division of Physical Biochemistry MRC National Institute for Medical Research London | UK | Biophysical Journal 92 G. Mashanov J. Molloy Automatic Detection of Single Fluoroph... | 2007 | |
| GPUgaussMLE gaussMLEv2 | Localization 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-IML | Localization | Marco Castello and Francesca Pennacchietti Istituto Italiano di Tecnologia | Italy | 2014 | |||
| GraspJ | Localization 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 |
| iNMF | Deconvolution | Matlab Open access | Ondrej Mandula Fondation Nanosciences Grenoble | France | Optics express 22.20 O. Mandula et al. Localisation microscopy with quantum dots ... | 2014 | |
| Insight3 | Localization Arbitrary LS | Stand-alone Commercial | Author 2013 | Ryan McGorty and Bo Huang Dept of Pharmaceutical Chemistry University of California San Francisco | USA | 2013 | |
| JD Localization | Localization | Matlab Open access | Josh Larkin University of Oxford Oxford | UK | Optics Express 20 J. Larkin P. Cook Maximum precision closed-form solution for... | 2012 | |
| LEAP | Localization 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 |
| L1H | Localization 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 |
| LAMA | Clustering | Stand-alone Open access | Sebastian Malkusch University Frankfurt | Germany | Scientific Reports 6 S. Malkusch M. Heilemann Extracting quantitative information... | 2016 | |
| LH-PALM | Localization | Registered | Chunqiang Li Unversity of Texas El Paso | USA | 2018 | ||
| livePALM2 | Localization | 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 |
| Localizer | Localization | Igor Open access | Expert 2016 | Department of Chemistry University of Leuven | Belgium | J. of Biomedical Optics 17 P. Dedecker et al. Localizer: fast accurate open-source and ... | 2012 |
| Loco_PALM | Localization | Registered | Johannes Hohlbein Wageningen University & Research | NL | 2015 | ||
| Lucky Imaging | Localization Lucky Image Gaussian | Brid Cronin Keble College Oxford | UK | Biophysical Journal 96 B. Cronin B. de Wet M. Wallace Lucky Imaging: Improved Local... | 2009 | ||
| M2LE | Localization 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 scripts | Localization | Matlab | Registered | Sheng Liu New York University | USA | 2017 | |
| MaLiang | Localization 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 |
| MIATool | Localization | Java Open access | Author 2016 | R. Velmurugan A. V. Abraham and R. J. Ober Texas A&M University College Station Texas | USA | IEEE Trans. Inf. Technol. Biomed. 14 J. Chao E.S. Ward R. J. Ober A software framework for the an... | 2010 |
| MicroManager LM | Localization 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 |
| mlePALM | Localization | Matlab | Author 2016 | Hendrik Deschout Laboratory of Nanoscale Biology EPFL | Swiss | 2016 | |
| MrSE | Localization 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 |
| MTT | Localization | Matlab Access on request | Centre d'Immunologie de Marseille-Luminy and Institut Fresnel Marseille | France | Nature Protocol Exchange Arnauld Serge Nicolas Bertaux Herve Rigneault and Didier Mar... | 2008 | |
| Octane | Localization Gaussian LS | ImageJ Open access | Expert 2013 2016 | University of Connecticut Health Center | USA | Biophysical Journal 4 Lili Niu and Ji Yu Investigating intracellular dynamics of F... | 2008 |
| palm3d | Localization | Python Open access | National Institute of Biomedical Imaging and Bioengineering National Institutes of Health Bethesda MD | USA | Nature Methods 8 A. York et al. Confined activation and subdiffractive locali... | 2011 | |
| PALMER | Localization | 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-PALM | Localization | Matlab | The Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda Maryland | USA | Nature Protocol Exchange 8 P. Prabuddha T. Jovanovic-Talisman J. Lippincott-Schwartz Qu... | 2013 | |
| PeakFit | Localization Gaussian LS | ImageJ Open access | Author 2013 2016 | Alex Herbert Genome Damage and Stability Centre University of Sussex | UK | 2013 | |
| PeakSelector | Localization Gaussian LS | IDL | Expert 2013 2016 | USA | PNAS 9 G. Shtengel et al. Interferometric fluorescent super-resolut... | 2009 | |
| Picasso | Localization | Python Open access | Molecular Imaging and Bionanotechnology - Max Plack Institute - Munich | Germany | Nature Protocols 12 J. Schnitzbauer et al. Super-resolution microscopy with DNA-... | 2017 | |
| Physics-Leiden | Localization | Matlab | Registered | Rolf Harkes Leiden University | NL | 2014 | |
| pSMLM-3D | Localization | 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 |
| PYME | Localization 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-STORM | Localization Gaussian MLE | ImageJ Later | Author 2016 | Luchang Li Wuhan National Laboratory | China | 2017 | |
| QuickPALM | Localization 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 |
| RadialSymmetry | Localization 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 |
| RainSTORM | Localization | 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 |
| RapidSTORM | Localization 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 |
| RmD | Localization | Registered | Mo Chen and Xiaolin Nan Oregon Health & Science University | USA | 2015 | ||
| SharpViSu | Clustering | Matlab Open access | L. Andronov Centre for Integrative Biology University of Strasbourg | France | Bioinformatics 32 L. Andronov SharpViSu: integrated analysis and segmentation ... | 2016 | |
| SHRImP | Localization | Department of Physics and Center for Biophysics and Computational Biology University of Illinois at Urbana-Champaign Urbana IL | USA | PNAS 101 M. Gordon T. Ha P. Selvin Single-molecule high-resolution im... | 2004 | ||
| SimplePALM | Localization 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 |
| SimpleSTORM | Localization 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 |
| SMALL-LABS | Localization | Matlab Open access | Julie Biteen University of Michigan | USA | Biophysical Journal 116 Isaacoff et al. SMALL-LABS: Measuring Single-Molecule Intens... | 2019 | |
| SMAP | Localization 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 |
| SMfit | Localization Integrated Gaussian ADCG | Julia / Python | Author 2016 | Hayato Ikoma Electrical Engineering Department Stanford University | USA | 2016 | |
| SMolPhot | Localization 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 | |
| SNSMIL | Localization 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 | |
| SOLAR_STORM | Localization 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 |
| SOSplugin | Localization Gaussian LS | ImageJ Open access | Author 2013 | Ihor Smal Erasmus MC - University Medical Center Rotterdam | NL | 2013 | |
| SPARCOM | Localization 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 |
| SparseFMM | Localization | Registered | Haowen Zhang Tsinghua University | China | 2015 | ||
| SparseSR | Localization | Gongguo Tong University of Wisconsin Madison | USA | 2013 | |||
| SR-Tesseler | Clustering | Stand-alone Open access | University of Bordeaux and Interdisciplinary Institute for Neuroscience | France | Nature Methods 12 F. Levet SR-Tesseler: a method to segment and quantify local... | 2016 | |
| STORMChaser | Localization | Matlab | Author 2016 | Anna Archetti Institute of Physics EPFL | Swiss | 2016 | |
| ThunderSTORM | Localization 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 |
| TVSTORM | Localization 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 FluoroBancroft | Localization 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 |
| WaveTracer | Localization 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 |
| WTM | Localization 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-3D | Localization 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