Directory of Single-Molecule Localization Microscopy Software

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/

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

3D-STORM Tools

• Affiliation: University of Upper Austria, Linz, Austria
• Contact: Fabian Hauser
• Challenge participation: 2016

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

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

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

Auto-Bayes

• Affiliation: National Center for Nanoscience and Technology, Beijing, China
• Link: http://english.nanoctr.cas.cn/dai/software/
• Contact: Yunqing Tang and Luru Dai
• Challenge participation: 2013

B-recs

• Affiliation: Janelia Farm Research Campus, HHMI, USA
• Link: https://github.com/hrouault/Brecs
• Contact: Herve Rouault
• Challenge participation: 2013, 2016

ClearPALM

• Affiliation: Laboratory of Nanoscale Biology, EPFL, Switzerland
• Contact: Arun Shivanandan
• Challenge participation: 2013

Cspline

• Affiliation: Harvard University, Xiaowei Zhuang, Harvard University, HHMI, USA
• Link: https://github.com/ZhuangLab/storm-analysis/tree/master/spliner
• Contact: Hazen Babcock
• Challenge participation: 2016

CSSTORM
FasterSTORM

• Affiliation: Department of Earth and Environment, Florida International University, Miami, USA
• Reference: L. Zhu, W. Zhang, D. Elnatan, B. Huang, FasterSTORM using compressed sensing, Nature Methods 9, 2012.
• Link: http://www.nature.com/nmeth/journal/v9/n7/abs/nmeth.1978.html
• Challenge participation: 2013

DAOSTORM

• Affiliation: Laboratory of Experimental Biophysics, EPFL, Switzerland
• Reference: S.J. Holden, S. Uphoff, A.N. Kapanidis, DAOSTORM: an algorithm for high density superresolution microscopy, Nature Methods 8, 2011.
• Link: http://www.physics.ox.ac.uk/users/kapanidis/group/Main.Software.html
• Contact: Seamus Holden
• Challenge participation: 2013

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

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

EM

• Affiliation: Department of Electrical Engineering, The City College of City University of New York, USA
• Contact: Yi Sun

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

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

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

FastSR

• Affiliation: Department of Biomedical Engineering and Department of Electrical Engineering, University at Buffalo, USA
• Contact: Yanhua Wang and Leslie Ying
• Challenge participation: Registered

FIRESTORM

• Affiliation: Institute of Biophysics, Ulm University, Germany
• Reference: M. Schoen e t al. TM (2016) Super-Resolution Microscopy Reveals Presynaptic Localization of the ALS/FTD Related Protein FUS in Hippocampal Neurons, Front. Cell. Neurosciences, 2016.
• Link: http://www.uni-ulm.de/nawi/nawi-biophys/forschung/forschung-michaelis/method-development/software/firestorm.html
• Contact: Thomas Vomhof and Jochen Reichel
• Challenge participation: 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/

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

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

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/

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

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

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

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

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

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

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

livePALM

• Affiliation: Institute of Applied Physics Karlsruhe Institute of Technology (KIT) Karlsruhe,
• Reference: P. N. Hedde et al., Online image analysis software for photoactivation localization microscopy, Nature Methods 6, 2009.
• Link: http://www.nature.com/nmeth/journal/v6/n10/suppinfo/nmeth1009-689_S1.html

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

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

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

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

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

MicroManager
LM

• Affiliation: Vale Lab, University of California, San Francisco, USA
• Reference: A. Edelstein et al., Advanced methods of microscope control using microManager software, Journal of Biological Methods 1(2), 2014.
• Link: http://valelab.ucsf.edu/~MM/MMwiki/index.php/Localization_Microscopy
• Contact: Nico Stuurman
• Challenge participation: 2013

mlePALM

• Affiliation: Laboratory of Nanoscale Biology, EPFL, Switzerland
• Challenge participation: 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

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.

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

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/

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

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.

PeakFit

• Affiliation: Genome Damage and Stability Centre, University of Sussex, UK
• Link: http://www.sussex.ac.uk/gdsc/intranet/microscopy/imagej/smlm_plugins
• Contact: Alex Herbert
• Challenge participation: 2013, 2016

PeakSelector

• Reference: G. Shtengel et al., Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure, PNAS 9, 2009.
• Challenge participation: 2013, 2016

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

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

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

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: Mikl—s ErdŽlyi
• Challenge participation: 2016

RapidSTORM

• Affiliation: Google Inc. and Biotechnologie and Biophysik, University of Wurzburg, Germany
• Reference: S. Wolter et al., rapidSTORM: accurate, fast open-source software for localization microscopy, Nature Methods 9, 2012.
• Link: http://www.super-resolution.biozentrum.uni-wuerzburg.de/research_topics/rapidstorm/
• Contact: Steve Wolter, Markus Sauer,
• Challenge participation: 2013, 2016

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

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.

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

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

SMAP

• Affiliation: EMBL, Heidelberg, Germany
• Challenge participation: 2016

SMfit

• Affiliation: Electrical Engineering Department, Stanford University, USA
• Contact: Hayato Ikoma, Gordon Wetzstein
• Challenge participation: 2016

SMolPhot

• Affiliation: University of Tartu, Institute of Physics,
• Link: http://www.molphot.com/
• Contact: Martti PŠrs, Ardi Loot, Andreas Valdmann, Marko Eltermann, Mihkel Kree
• Challenge participation: 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

SOSplugin

• Affiliation: Erasmus MC - University Medical Center Rotterdam, The Netherlands
• Link: http://smal.ws/home/Software
• Contact: Ihor Smal Erik Meijering
• Challenge participation: 2013

SparseFMM

• Affiliation: Tsinghua University, China
• Contact: Haowen Zhang
• Challenge participation: Registered

SparseSR

• Affiliation: University of Wisconsin, Madison, USA
• Contact: Gongguo Tong
• Challenge participation: Registered

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

STORMChaser

• Affiliation: Institute of Physics, EPFL, Switzerland
• Contact: Anna Archetti
• Challenge participation: 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

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

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

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

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