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Single-Molecule Localization Microscopy  •  Software Benchmarking

Directory of Single-Molecule Localization Microscopy Software

These software are mainly performed the tasks of detection and accurate localization of the blinking molecules. There are two type of reconstruction methods: the localization methods which provide a explicit list of positions of the molecules and the deconvolution methods which reconstructs an super-resolved image without explicit localization. The last ones are typically for high density imaging conditions. We present also some software that are dedicated to the post-processing, e.g. rendering or clustering.

We are trying to maintain up to date a list of the software that are related to SMLM / PALM / STORM. In case, you have additional information, please contact us.

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70 SMLM software sorted by name

3B
  • Affiliation: Randall Division of Cell and Molecular Biophysics at the Kings College, London, UK
  • Reference: E. Rosten,G. Jones, S. Cox, ImageJ plug-in for Bayesian analysis of blinking and bleaching, Nature Methods 10, 2013.
  • Link: http://www.coxphysics.com/3b/
Deconvolution
ImageJ
Open access
2013
3D-DAOSTORM
  • Affiliation: Harvard University (Zhuang group), Cambridge, MA, USA
  • Reference: Hazen Babcock, Yaron Sigal and Xiaowei Zhuang, A high-density 3D localization algorithm for stochastic optical reconstruction microscopy, Optical Nanoscopy 1, 2012.
  • Link: http://zhuang.harvard.edu/software/3d_daostorm.html
  • Contact: Hazen Babcock
  • Challenge participation: 2013
Localization
Python
Open access
High-density
2012
3D-STORM Tools
  • Affiliation: University of Upper Austria, Linz, Austria
  • Contact: Fabian Hauser
  • Challenge participation: 2016
Localization
Qt framework
Proprietary
a-livePALM
  • Affiliation: Institute of Applied Physics Karlsruhe Institute of Technology (KIT) Karlsruhe, Germany
  • Reference: Y. Li et al. Fast and efficient molecule detection in localization-based super-resolution microscopy by parallel adaptive histogram equalization, ACS Nano 7, 2013.
  • Link: http://www.aph.kit.edu/nienhaus/english/26_116.php
  • Contact: Yiming Li
  • Challenge participation: 2013
Localization
Matlab
Access on request
2013
ADCG
  • Affiliation: University of Berkeley, USA
  • Reference: N. Boyd, G. Schiebinger, B. Recht, The Alternating Descent Conditional Gradient Method for Sparse Inverse Problems, arXiv, 2015.
  • Link: https://github.com/nboyd/SparseInverseProblems.jl
  • Contact: Nicholas Boyd
  • Challenge participation: 2016
Localization
Julia
Open access
High-density
2015
ALOHA
  • Affiliation: Bio-Imaging and Signal Processing Lab, KAIST, Korea
  • Reference: Min, Junhong, Fast live cell imaging at nanometer scale using annihilating filter based low rank Hankel matrix approach, SPIE Optical Engineering, 2015.
  • Contact: Junhong Min, Kyong Jin
  • Challenge participation: 2016
Deconvolution
Matlab
2015
Auto-Bayes
Localization
Stand-alone
Open access
2015
B-recs
Localization
Stand-alone
Open access
2013
ClearPALM
  • Affiliation: Laboratory of Nanoscale Biology, EPFL, Switzerland
  • Contact: Arun Shivanandan
  • Challenge participation: 2013
Localization
Matlab
2007
Cspline
Localization
Python
Open access
2016
CSSTORM
FasterSTORM
Deconvolution
Matlab
Open access
High-density
2012
DAOSTORM
Localization
Python
Open access
High-density
2011
DeconSTORM
  • Affiliation: Havard University (Zhuang group), Cambridge, MA, USA
  • Reference: E. A. Mukamel, H. Babcock, X. Zhuang, Statistical Deconvolution for Superresolution Fluorescence Microscopy, Biophysical Journal 102, 2012.
  • Link: http://zhuang.harvard.edu/software/decon_storm.html
  • Contact: Eran Mukamel
Deconvolution
Matlab
Open access
2012
Easy-DHPSF
  • Affiliation: Stanford University Department of Chemistry, Stanford, USA
  • Reference: M. Lew et al., Easy-DHPSF open-source software for three-dimensional localization of single molecules with precision beyond the optical diffraction limit, Nature Protocol Exchange, 2013.
  • Link: https://sourceforge.net/projects/easy-dhpsf/
  • Contact: Alex von Diezmann, Camille Bayas, and W. E. Moerner
  • Challenge participation: 2016
Localization
Matlab
Open Access
Double-Helix
2013
EM
  • Affiliation: Department of Electrical Engineering, The City College of City University of New York, USA
  • Contact: Yi Sun
Localization 2D and 3D
2016
FacePALM
  • Affiliation: Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
  • Reference: E. Hoogendoorn et al., Image deconvolution techniques with robust background estimation applied to photactivation localization microscopy (PALM), Focus On Microscopy Conference (FOM'13), Maastricht, The Netherlands, 2013.
  • Contact: Eelco Hoogendoorn
  • Challenge participation: 2013
Deconvolution
2013
FALCON
  • Affiliation: Bio-Imaging and Signal Processing Lab, KAIST, Republic of Korea
  • Reference: Junhong Min et al., FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data, Scientific Reports 4, 2014.
  • Link: http://bispl.weebly.com/nanoscopy.html
  • Contact: Junhong Min and Jong Chul Ye
  • Challenge participation: 2013, 2016
Localization
Matlab
Open access
High-density
2014
Fast-ML-HD
  • Affiliation: Bio-Imaging and Signal Processing Lab, KAIST, Republic of Korea
  • Reference: K.S. Kim et al., Fast maximum likelihood high-density low-SNR super-resolution localization microscopy, SampTA'13 Conference Bremen, 2013.
  • Contact: Kyungsang Kim and Jong Chul Ye
  • Challenge participation: 2013
Localization
Matlab
High-density
2013
FastSR
  • Affiliation: Department of Biomedical Engineering and Department of Electrical Engineering, University at Buffalo, USA
  • Contact: Yanhua Wang and Leslie Ying
  • Challenge participation: Registered
Localization
2013
FIRESTORM
Localization
Matlab
2016
FOCAL
  • Affiliation: Department of Physics, University of Toronto, Toronto, Canada
  • Reference: A. Mazouchi J. N. Milstein, Fast Optimized Cluster Algorithm for Localizations (FOCAL): a spatial cluster analysis for super-resolved microscopy, Bioinformatics, 2016.
  • Link: http://www.utm.utoronto.ca/milsteinlab/resources/Software/FOCAL/
Clustering
Matlab
Open access
2016
FPGA
SFP Estimator
  • Affiliation: Heidelberg University, Germany
  • Reference: F. Gruell et al., Accelerating Image Analysis for Localization Microscopy with FPGAs, International Conference on Field Programmable Logic and Applications (FPL), 2011.
  • Link: https://github.com/ManfredKi/SFP-Estimator
  • Contact: Manfred Kirchgessner and Frederik Gruell
  • Challenge participation: 2013, 2016
Localization
Stand-alone
Open-access
2011
Gauss2dcirc
  • Affiliation: University of Illinois, Urbana, Illinois, USA
  • Reference: S.M. Anthony, S. Granick, Image analysis with rapid and accurate two-dimensional Gaussian fitting, Langmuir 25, 2009.
  • Link: http://groups.mrl.uiuc.edu/granick/software.html
  • Contact: Stephen Anthony
  • Challenge participation: 2013
Localization
Matlab
Open access
2009
GMIMPRO
  • Affiliation: Division of Physical Biochemistry, MRC National Institute for Medical Research, London, UK
  • Reference: G. Mashanov, J. Molloy, Automatic Detection of Single Fluorophores in Live Cells, Biophysical Journal 92, 2007.
  • Link: http://www.mashanov.uk/
Localization
ImageJ
Open access
2007
GPUgaussMLE
gaussmlev2
  • Affiliation: Delft University of Technology, The Netherlands
  • Reference: C.S. Smith et al., Fast, single-molecule localization that achieves theoretically minimum uncertainty, Nature Methods 7, 2010.
  • Link: http://panda3.phys.unm.edu/~klidke/software.html
  • Contact: Keith Lidke and Bernd Rieger
  • Challenge participation: 2013
Localization
Matlab
Open access
2010
GraspJ
  • Affiliation: ICFO-Institut de Ciencies Fotoniques, Barcelona, Spain
  • Reference: N. Brede and M. Lakadamyali, GraspJ: an open source, real-time analysis package for super-resolution imaging, Optical Nanoscopy 1, 2012.
  • Link: http://code.google.com/p/graspj/
  • Contact: Norman Brede and Melike Lakadamyali,
  • Challenge participation: 2013
Localization
ImageJ
Open access
2012
iNMF
  • Affiliation: Fondation Nanosciences, Grenoble, France
  • Reference: O. Mandula et al., Localisation microscopy with quantum dots using non-negative matrix factorisation, Optics express 22.20, 2014.
  • Link: https://github.com/aludnam/inmf
  • Contact: Ondrej Mandula
Deconvolution
2014
Insight3
  • Affiliation: Dept of Pharmaceutical Chemistry, University of California, San Francisco, USA
  • Link: http://huanglab.ucsf.edu/STORM.html
  • Contact: Ryan McGorty and Bo Huang
  • Challenge participation: 2013
Localization
Stand-alone
Commercial
2013
JD Localization
  • Affiliation: University of Oxford, Oxford, UK
  • Reference: J. Larkin, P. Cook, Maximum precision closed-form solution for localizing diffraction-limited spots in noisy images, Optics Express 20, 2012.
  • Contact: Josh Larkin
Localization
2012
L1H
  • Affiliation: Harvard University, Cambridge, MA, USA
  • Reference: Hazen Babcock, Jeff Moffit, Yunlong Cao and Xiaowei Zhuang, Fast compressed sensing analysis for super-resolution imaging using L1-homotopy, Optics Express 21, 2013.
  • Link: http://zhuang.harvard.edu/software/l1h.html
  • Contact: Hazen Babcock
  • Challenge participation: 2013, 2016
Deconvolution
Python
Open access
High-density
2013
LAMA
  • Affiliation: University Frankfurt, Germany
  • Reference: S. Malkusch, M. Heilemann, Extracting quantitative information from single-molecule super-resolution imaging data with LAMA - LocAlization Microscopy Analyzer, Scientific Reports 6, 2016.
  • Link: http://user.uni-frankfurt.de/~malkusch/lama.html
  • Contact: Sebastian Malkusch
Post-processing
Open access
2016
livePALM
Localization
Germany
Matlab
2009
Localizer
  • Affiliation: Department of Chemistry, University of Leuven, Belgium
  • Reference: P. Dedecker et al., Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy, Journal of Biomedical Optics 17, 2012.
  • Link: http://www.igorexchange.com/project/Localizer
  • Challenge participation: 2016
Localization
Igor
Open access
2012
Lucky Imaging
  • Affiliation: Keble College, Oxford, UK
  • Reference: B. Cronin, B. de Wet, M. Wallace, Lucky Imaging: Improved Localization Accuracy for Single Molecule Imaging, Biophysical Journal 96, 2009.
  • Contact: Brid Cronin
Localization
2009
M2LE
  • Affiliation: California State Polytechnic University, Pomona, USA
  • Reference: R. Starr, S. Stahlheber and A. Small, Fast maximum likelihood algorithm for localization of fluorescent molecules, Optics Letters 37, 2012.
  • Link: http://code.google.com/p/molecule-localization-plugin/
  • Contact: Shane Stahlheber and Alex Small
  • Challenge participation: 2013
Localization
ImageJ
Open access
2012
MaLiang
  • Affiliation: Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
  • Reference: T. Quan et al., Ultra-fast, high-precision image analysis for localization-based super resolution microscopy, Optics Express 11, 2010.
  • Link: http://bmp.hust.edu.cn/srm/
  • Contact: Zhen-li Huang and Yujie Wang
  • Challenge participation: 2013, 2016
Localization
ImageJ
Open access
2010
MIATool
  • Affiliation: Texas A&M University, College Station, Texas, USA
  • Reference: A. Tahmasbi, E.S. Ward, R.J. Ober, Determination of localization accuracy based on experimentally acquired image sets: applications to single molecule microscopy, Optics Express, 23, 2015.
  • Contact: R. J. Ober, A. V. Abraham, D. Kim, S. You], D. Kim, R. Velmurugan, M. R. Vahid, W. Kim, T. Islam, J. Chao
  • Challenge participation: 2016
Localization
Java
Open access
2015
MicroManager
LM
Localization
ImageJ
Open access
2014
mlePALM
  • Affiliation: Laboratory of Nanoscale Biology, EPFL, Switzerland
  • Challenge participation: 2016
Localization
Matlab
2016
MrSE
  • Affiliation: Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
  • Reference: H. Ma, F. Long, S. Zeng, and Z.-L. Huang, Fast and precise algorithm based on maximum radial symmetry for single molecule localization, Optics Letters 37, 2012.
  • Link: http://bmp.hust.edu.cn/srm/
  • Contact: Zhen-li Huang and Yi-na Wang
Localization
Stand-alone
2012
MTT
  • Affiliation: Centre d'Immunologie de Marseille-Luminy and Institut Fresnel, Marseille, France
  • Reference: Arnauld Serge, Nicolas Bertaux, Herve Rigneault and Didier Marguet, Multiple-target tracing (MTT) algorithm probes molecular dynamics at cell surface, Nature Protocol Exchange, 2008.
Localization
Matlab
2008
Octane
  • Affiliation: University of Connecticut Health Center, USA
  • Reference: Lili Niu and Ji Yu, Investigating intracellular dynamics of FtsZ cytoskeleton with photoactivation single-molecule tracking, Biophysical Journal 4, 2008.
  • Link: https://github.com/jiyuuchc/Octane
  • Challenge participation: 2013, 2016
Localization
ImageJ
Open access
2008
palm3d
  • Affiliation: National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
  • Reference: A. York et al., Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes, Nature Methods 8, 2011.
  • Link: http://code.google.com/p/palm3d/
Localization
Python
Open access
2011
PALMER
  • Affiliation: Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
  • Reference: Y. Wang, T. Quan, S. Zeng, Z.L. Huang, PALMER: a method capable of parallel localization of multiple emitters for high-density localization microscopy, Optics Express 14, 2012.
  • Link: http://bmp.hust.edu.cn/srm/
  • Contact: Zhen-li Huang and Yi-na Wang
  • Challenge participation: 2016
Localization
ImageJ
Open access
High-density
2012
PC-PALM
  • Affiliation: The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
  • Reference: P. Prabuddha, T. Jovanovic-Talisman, J. Lippincott-Schwartz, Quantifying spatial organization in point-localization superresolution images using pair correlation analysis, Nature Protocol Exchange 8, 2013.
Localization
Matlab
2013
PeakFit
Localization
ImageJ
Open access
2013
PeakSelector
  • Reference: G. Shtengel et al., Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure, PNAS 9, 2009.
  • Challenge participation: 2013, 2016
Localization
Matlab, IDL
2009
PYME
  • Affiliation: Nanobiology Institute, Yale University, West Haven, USA and University of Auckland, Auckland, New Zealand
  • Reference: D. Baddeley, M.B. Cannell, C. Soeller, Three-dimensional sub-100 nm super-resolution imaging of biological samples using a phase ramp in the objective pupil, Nano Research, 2011.
  • Link: http://code.google.com/p/python-microscopy
  • Contact: David Baddeley,
  • Challenge participation: 2013
Localization
Python
Open access
2011
QuickPALM
  • Affiliation: Institut Pasteur, Paris, France
  • Reference: R. Henriques et al., QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ, Nature Methods 7, 2010.
  • Link: https://code.google.com/p/quickpalm/
  • Contact: Ricardo Henriques and Christophe Zimmer,
  • Challenge participation: 2013, 2016
Localization
ImageJ
Open access
2010
RadialSymmetry
  • Affiliation: Department of Physics, The University of Oregon, USA
  • Reference: R. Parthasarathy, Rapid, accurate particle tracking by calculation of radial symmetry centers, Nature Methods 9, 2012.
  • Link: http://physics.uoregon.edu/~raghu/particle_tracking.html
  • Contact: Raghuveer Parthasarathy
  • Challenge participation: 2013
Localization
Matlab
Open access
2012
RainSTORM
  • Affiliation: University of Cambridge UK & University of Szeged, Hungary, UK
  • Reference: E.J. Rees et al., Elements of image processing in localisation microscopy, Journal of Optics 15, 2013.
  • Link: http://laser.cheng.cam.ac.uk/wiki/index.php/Resources
  • Contact: Mikls Erdlyi
  • Challenge participation: 2016
Localization
Matlab
Open access
2013
RapidSTORM
Localization
Stand-alone
Open access
2012
SharpViSu
  • Affiliation: Centre for Integrative Biology, University of Strasbourg, France
  • Reference: L. Andronov, SharpViSu: integrated analysis and segmentation of super-resolution microscopy data, Bioinformatics, 2016.
  • Link: https://github.com/andronovl/SharpViSu
  • Contact: L. Andronov
Post-processing
Matlab
Open access
2016
SHRImP
  • Affiliation: Department of Physics and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
  • Reference: M. Gordon, T. Ha, P. Selvin, Single-molecule high-resolution imaging with photobleaching, PNAS 101, 2004.
Localization
2004
SimplePALM
  • Affiliation: Institut Curie, Paris, and Centre de genetique moleculaire, Gif-sur-Yvette, France
  • Reference: J. Boulanger and al., Patch-based non-local functional for denoising fluorescence microscopy image sequences, IEEE Trans. on Medical Imaging 29, 2010.
  • Contact: Jerome Boulanger and Leila Muresan,
  • Challenge participation: 2013
Localization
Stand-alone
2010
SimpleSTORM
  • Affiliation: Heidelberg Collaboratory for Image Processing, Germany
  • Reference: U. Koethe, F. Herrmannsdoerfer, I. Kats, F.A. Hamprecht, SimpleSTORM: a fast, self-calibrating reconstruction algorithm for localization microscopy, Histochemistry and Cell Biology, 2014.
  • Link: https://github.com/ukoethe/simple-STORM.git
  • Contact: Ullrich Koethe and Luca Fiaschi
  • Challenge participation: 2013
Localization
Stand-alone
Open access
2014
SMAP
  • Affiliation: EMBL, Heidelberg, Germany
  • Challenge participation: 2016
Localization
Matlab
2016
SMfit
  • Affiliation: Electrical Engineering Department, Stanford University, USA
  • Contact: Hayato Ikoma, Gordon Wetzstein
  • Challenge participation: 2016
Localization
Julia
2016
SMolPhot
  • Affiliation: University of Tartu, Institute of Physics,
  • Link: http://www.molphot.com/
  • Contact: Martti Prs, Ardi Loot, Andreas Valdmann, Marko Eltermann, Mihkel Kree
  • Challenge participation: 2016
Localization
Stand-alone
Open access
2016
SNSMIL
  • Affiliation: Chongqing University, Chongqing and National Center for Nanoscience and Technology, Beijing, China
  • Link: http://english.nanoctr.cas.cn/dai/software/
  • Contact: Yunqing Tang, Luru Dai,
  • Challenge participation: 2013
Localization
Stand-alone
Open access
2013
SOSplugin
  • Affiliation: Erasmus MC - University Medical Center Rotterdam, The Netherlands
  • Link: http://smal.ws/home/Software
  • Contact: Ihor Smal Erik Meijering
  • Challenge participation: 2013
Localization
ImageJ
Open access
2013
SparseFMM
  • Affiliation: Tsinghua University, China
  • Contact: Haowen Zhang
  • Challenge participation: Registered
Localization
2015
SparseSR
  • Affiliation: University of Wisconsin, Madison, USA
  • Contact: Gongguo Tong
  • Challenge participation: Registered
Localization
2013
SR-Tesseler
  • Affiliation: University of Bordeaux and Interdisciplinary Institute for Neuroscience, Bordeaux, France
  • Reference: F. Levet, SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data, Nature Methods 12, 2016.
  • Link: http://www.iins.u-bordeaux.fr/team-sibarita-SR-Tesseler?lang=en
Rendering
Stand-alone
Open access
2016
STORMChaser
  • Affiliation: Institute of Physics, EPFL, Switzerland
  • Contact: Anna Archetti
  • Challenge participation: 2016
Localization
Matlab
2016
ThunderSTORM
  • Affiliation: Charles University, Prague, Czech Republic
  • Reference: M. Ovesny and al., ThunderSTORM: a comprehensive ImageJ plugin for PALM and STORM data analysis and super-resolution imaging, Bioinformatics, 2014.
  • Link: http://code.google.com/p/thunder-storm/
  • Contact: Guy Hagen, Pavel Krizek
  • Challenge participation: 2013, 2016
Localization
ImageJ
Open access
2014
TVSTORM
  • Affiliation: The Ohio State University, Columbus, OH, USA
  • Reference: J. Huang, S. Mingzhai, C. Yuejie, Super-resolution image reconstruction for high-density 3D single-molecule microscopy, ISBI 2016, 2016.
  • Contact: Jiaqing Huang,
  • Challenge participation: 2016
Localization
Matlab
2016
Wavelet
FluoroBancroft
  • Affiliation: Boston University, USA
  • Reference: S.B. Andersson, Localization of a fluorescent source without numerical fitting, Optics Express 16, 2008.
  • Link: http://www.bu.edu/anderssonlab/
  • Contact: Sean Andersson and, Trevor Ashley
  • Challenge participation: 2013
Localization
Matlab
Access on request
2008
WaveTracer
  • Affiliation: University of Bordeaux and Interdisciplinary Institute for Neuroscience, Bordeaux, France
  • Reference: A. Kechkar, D. Nair, M. Heilemann, D. Choquet, J.-B. Sibarita, Real-time analysis and visualization for single-molecule based super-resolution microscopy, PLoS One 8, 2013.
  • Contact: Adel Kechkar and Jean-Baptiste Sibarita
  • Challenge participation: 2013, 2016
Localization
Metamorph
Commercial
2013
WTM
3D-WTM
  • Affiliation: Hamamatsu Photonics K.K., Japan
  • Reference: S. Watanabe et al, Evaluation of Localization Algorithm of High-Density Fluorophores, Wedged Template Matching, Focus on Microscopy Conference (FOM'13) Maastricht, 2013.
  • Contact: Tomochika Takeshima and Shigeo Watanabe
  • Challenge participation: 2013, 2016
Localization
Stand-alone
High-density
2013

© 2016 Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
Last update: 19 Aug 2016