Directory of SMLM softwareThis 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 |
|---|---|---|---|---|---|---|---|
| 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 anal... | 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 localizat... | 2012 |
| 3D-STORM Tools | Localization | Qt framework Proprietary | Fabian Hauser University of Upper Austria, Linz | Austria | 2016 | ||
| 3D-WTM | Localization Wedge Matching | Stand-alone | Shigeo Watanabe Hamamatsu Photonics K.K. | Japan | FOM 2013 S. Watanabe et al, Evaluation of Localization Algorithm of H... | 2013 | |
| ADCG | Localization 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-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 usin... | 2015 |
| 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 Université Grenoble-Alpes, Grenoble | France | GRETSI Conf. 2015 R. Bacher, F. Chatelain, L. Guyon, Approche bayésienne non ... | 2015 | |
| C2SI | Localization | Registered | Oron Solomon Technion - Israel Institute of Technology | Israel | 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-Féraud, High density mole... | 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... | 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 co... | 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 algorit... | 2011 |
| DeepSTORM | Localization | Registered | Artur Speiser Neural System Analysis, Caesar, Bonn | Germany | 2017 | ||
| 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 Deconvolut... | 2012 | |
| Easy-DHPSF | Localization 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 |
| 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 r... | 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-SN... | 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 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 |
| 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 Localizati... | 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 accu... | 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 Fluoro... | 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 a... | 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-ti... | 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 f... | 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. Vetter... | 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, ... | 2013 |
| LAMA | Clustering | Stand-alone Open access | Sebastian Malkusch University Frankfurt | Germany | Scientific Reports 6 S. Malkusch, M. Heilemann, Extracting quantitative informati... | 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 photo... | 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, ... | 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 Lo... | 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 likelihoo... | 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 fo... | 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 | Optics Express, 23 A. Tahmasbi, E.S. Ward, R.J. Ober, Determination of localiza... | 2015 |
| 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 ... | 2014 |
| mlePALM | Localization | Matlab | Autthor 2016 | 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 a... | 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 M... | 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 ... | 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 local... | 2011 | |
| PALMER | Localization | 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-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,... | 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 | USA | PNAS 9 G. Shtengel et al., Interferometric fluorescent super-resolu... | 2009 | |
| Physics-Leiden | Localization | Matlab | Registered | Rolf Harkes Leiden University | NL | 2014 | |
| 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... | 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 calcu... | 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 localisati... | 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 sof... | 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... | 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 d... | 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, Sim... | 2014 |
| SMAP | Localization Gaussian MLE, radial symmetry | Matlab | Author 2016 | Jonas Ries EMBL, Heidelberg | Germany | 2016 | |
| SMfit | Localization Integrated Gaussian ADCG | Julia / Python | Author 2016 | Hayato Ikoma Electrical Engineering Department, Stanford University | USA | 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 | |
| SMolPhot | Localization Gaussian LS | Python / C Open access | Author 2016 | Martti Pars and Ardi Loot University of Tartu, Institute of Physics | Estonia | 2016 | |
| SOLAR_STORM | Localization L1-Homotopy | Matlab / C | Author 2016 | Yoon J. Jung and Nikta Fakhri Fakri Lab, MIT | USA | 2016 | |
| SOSplugin | Localization Gaussian LS | ImageJ Open access | Author 2013 | Ihor Smal Erasmus MC - University Medical Center Rotterdam | NL | 2013 | |
| 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 loca... | 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 plug... | 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 rec... | 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. Sibarit... | 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 H... | 2013 |
© 2017
Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 31 Mar 2017