The DOI matches its Crossref record; 56 of the 56 references it cites were found in a registry or an index.
Quantitative evaluation of software packages for single-molecule localization microscopy
Open accessOverview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Imaging Intracellular Fluorescent Proteins at Nanometer Resolution
Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S., Bonifacino, J. S., Davidson, M. W., Lippincott-Schwartz, J., & Hess, H. F. (2006) · Science · doi:10.1126/science.1127344 · Cited by 8,772
Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)
Rust, M. J., Bates, M., & Zhuang, X. (2006) · Nature Methods · doi:10.1038/nmeth929 · Cited by 8,078
Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy
Hess, S. T., Girirajan, T. P. K., & Mason, M. D. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.091116 · Cited by 3,605
Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy
Huang, B., Wang, W., Bates, M., & Zhuang, X. (2008) · Science · doi:10.1126/science.1153529 · Cited by 2,796
Rosenthal, P. B., & Henderson, R. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.07.013 · Cited by 2,416
Precise Nanometer Localization Analysis for Individual Fluorescent Probes
Thompson, R. E., Larson, D. R., & Webb, W. W. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75618-x · Cited by 2,320
Ovesný, M., Křížek, P., Borkovec, J., Švindrych, Z., & Hagen, G. M. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu202 · Cited by 1,506
A guide to super-resolution fluorescence microscopy
Schermelleh, L., Heintzmann, R., & Leonhardt, H. (2010) · Journal of Cell Biology · doi:10.1083/jcb.201002018 · Cited by 1,255
Pavani, S. R. P., Thompson, M. A., Biteen, J. S., Lord, S. J., Liu, N., Twieg, R. J., Piestun, R., & Moerner, W. E. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900245106 · Cited by 1,040
Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure
Shtengel, G., Galbraith, J. A., Galbraith, C. G., Lippincott-Schwartz, J., Gillette, J. M., Manley, S., Sougrat, R., Waterman, C. M., Kanchanawong, P., Davidson, M. W., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0813131106 · Cited by 888
Self-citationOptimized localization analysis for single-molecule tracking and super-resolution microscopy
Mortensen, K. I., Churchman, L. S., Spudich, J. A., & Flyvbjerg, H. (2010) · Nature Methods · doi:10.1038/nmeth.1447 · Cited by 871
Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples
Juette, M. F., Gould, T. J., Lessard, M. D., Mlodzianoski, M. J., Nagpure, B. S., Bennett, B. T., Hess, S. T., & Bewersdorf, J. (2008) · Nature Methods · doi:10.1038/nmeth.1211 · Cited by 812
Measuring image resolution in optical nanoscopy
Nieuwenhuizen, R. P. J., Lidke, K. A., Bates, M., Puig, D. L., Grünwald, D., Stallinga, S., & Rieger, B. (2013) · Nature Methods · doi:10.1038/nmeth.2448 · Cited by 800
Localization Accuracy in Single-Molecule Microscopy
Ober, R. J., Ram, S., & Ward, E. S. (2004) · Biophysical Journal · doi:10.1016/s0006-3495(04)74193-4 · Cited by 587
Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithms
Huang, F., Hartwich, T. M. P., Rivera-Molina, F. E., Lin, Y., Duim, W. C., Long, J. J., Uchil, P. D., Myers, J. R., Baird, M. A., Mothes, W., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2488 · Cited by 526
Fast, single-molecule localization that achieves theoretically minimum uncertainty
Smith, C. S., Joseph, N., Rieger, B., & Lidke, K. A. (2010) · Nature Methods · doi:10.1038/nmeth.1449 · Cited by 522
Faster STORM using compressed sensing
Zhu, L., Zhang, W., Elnatan, D., & Huang, B. (2012) · Nature Methods · doi:10.1038/nmeth.1978 · Cited by 518
Precisely and accurately localizing single emitters in fluorescence microscopy
Deschout, H., Zanacchi, F. C., Mlodzianoski, M., Diaspro, A., Bewersdorf, J., Hess, S. T., & Braeckmans, K. (2014) · Nature Methods · doi:10.1038/nmeth.2843 · Cited by 498
Rapid, accurate particle tracking by calculation of radial symmetry centers
Parthasarathy, R. (2012) · Nature Methods · doi:10.1038/nmeth.2071 · Cited by 447
DAOSTORM: an algorithm for high- density super-resolution microscopy
Holden, S. J., Uphoff, S., & Kapanidis, A. N. (2011) · Nature Methods · doi:10.1038/nmeth0411-279 · Cited by 440
New directions in single-molecule imaging and analysis
Moerner, W. E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610081104 · Cited by 440
Bayesian localization microscopy reveals nanoscale podosome dynamics
Cox, S., Rosten, E., Monypenny, J., Jovanović‐Talisman, T., Burnette, D. T., Lippincott‐Schwartz, J., Jones, G. E., & Heintzmann, R. (2011) · Nature Methods · doi:10.1038/nmeth.1812 · Cited by 432
QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ
Henriques, R., Lelek, M., Fornasiero, E. F., Valtorta, F., Zimmer, C., & Mhlanga, M. M. (2010) · Nature Methods · doi:10.1038/nmeth0510-339 · Cited by 411
Fourier ring correlation as a resolution criterion for super-resolution microscopy
Banterle, N., Bui, K. H., Lemke, E. A., & Beck, M. (2013) · Journal of Structural Biology · doi:10.1016/j.jsb.2013.05.004 · Cited by 366
Fluorophore localization algorithms for super-resolution microscopy
Small, A., & Stahlheber, S. (2014) · Nature Methods · doi:10.1038/nmeth.2844 · Cited by 349
Simultaneous multiple-emitter fitting for single molecule super-resolution imaging
Huang, F., Schwartz, S. L., Byars, J. M., & Lidke, K. A. (2011) · Biomedical Optics Express · doi:10.1364/boe.2.001377 · Cited by 311
Patch-Based Nonlocal Functional for Denoising Fluorescence Microscopy Image Sequences
Boulanger, J., Kervrann, C., Bouthemy, P., Elbau, P., Sibarita, J.-B., & Salamero, J. (2010) · IEEE Transactions on Medical Imaging · doi:10.1109/tmi.2009.2033991 · Cited by 281
3‐D PSF fitting for fluorescence microscopy: implementation and localization application
KIRSHNER, H., AGUET, F., SAGE, D., & UNSER, M. (2013) · Journal of Microscopy · doi:10.1111/j.1365-2818.2012.03675.x · Cited by 277
Self-citationJanesick, J. R. (2007) · SPIE eBooks · doi:10.1117/3.725073 · Cited by 273
Holden, S. J., Pengo, T., Meibom, K. L., Fernandez Fernandez, C., Collier, J., & Manley, S. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313368111 · Cited by 197
Self-citationWang, Y., Schnitzbauer, J., Hu, Z., Li, X., Cheng, Y., Huang, Z.-L., & Huang, B. (2014) · Optics Express · doi:10.1364/oe.22.015982 · Cited by 190
A high-density 3D localization algorithm for stochastic optical reconstruction microscopy
Babcock, H. P., Sigal, Y. M., & Zhuang, X. (2012) · Optical Nanoscopy · doi:10.1186/2192-2853-1-6 · Cited by 178
Statistical Deconvolution for Superresolution Fluorescence Microscopy
Mukamel, E. A., Babcock, H. P., & Zhuang, X. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.03.070 · Cited by 177
Image Analysis with Rapid and Accurate Two-Dimensional Gaussian Fitting
Anthony, S. M., & Granick, S. (2009) · Langmuir · doi:10.1021/la900393v · Cited by 171
Real-Time Analysis and Visualization for Single-Molecule Based Super-Resolution Microscopy
Kechkar, A., Nair, D. K., Heilemann, M., Choquet, D., & Sibarita, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062918 · Cited by 164
Quantitative study of single molecule location estimation techniques
Abraham, A. V., Ram, S., Chao, J., Ward, E. S., & Ober, R. J. (2009) · Optics Express · doi:10.1364/oe.17.023352 · Cited by 158
Niu, L., & Yu, J. H. (2008) · Biophysical Journal · doi:10.1529/biophysj.108.128751 · Cited by 153
FALCON: fast and unbiased reconstruction of high-density super-resolution microscopy data
Min, J., Vonesch, C., Kirshner, H., Carlini, L., Olivier, N., Holden, S. J., Manley, S., Ye, J. C., & Unser, M. A. (2014) · Scientific Reports · doi:10.1038/srep04577 · Cited by 153
Self-citationHandbook of Single-Molecule Biophysics
Hinterdorfer, P., & van Oijen, A. M. (2009) · Springer eBooks · doi:10.1007/978-0-387-76497-9 · Cited by 145
Visualization of Localization Microscopy Data
Baddeley, D., Cannell, M. B., & Soeller, C. (2010) · Microscopy and Microanalysis · doi:10.1017/s143192760999122x · Cited by 142
The Lateral and Axial Localization Uncertainty in Super‐Resolution Light Microscopy
Rieger, B., & Stallinga, S. (2013) · ChemPhysChem · doi:10.1002/cphc.201300711 · Cited by 129
A call for bioimaging software usability
Carpenter, A. E., Kamentsky, L. D., & Eliceiri, K. W. (2012) · Nature Methods · doi:10.1038/nmeth.2073 · Cited by 126
Localization microscopy coming of age: from concepts to biological impact
Sauer, M. (2013) · Journal of Cell Science · doi:10.1242/jcs.123612 · Cited by 99
Fast compressed sensing analysis for super-resolution imaging using L1-homotopy
Babcock, H. P., Moffitt, J. R., Cao, Y., & Zhuang, X. (2013) · Optics Express · doi:10.1364/oe.21.028583 · Cited by 80
Ultra-fast, high-precision image analysis for localization-based super resolution microscopy
Quan, T., Li, P., Long, F., Zeng, S., Luo, Q., Hedde, P. N., Nienhaus, G. U., & Huang, Z. (2010) · Optics Express · doi:10.1364/oe.18.011867 · Cited by 79
Measuring localization performance of super-resolution algorithms on very active samples
Wolter, S., Endesfelder, U., van de Linde, S., Heilemann, M., & Sauer, M. (2011) · Optics Express · doi:10.1364/oe.19.007020 · Cited by 76
Localization of a fluorescent source without numerical fitting
Andersson, S. B. (2008) · Optics Express · doi:10.1364/oe.16.018714 · Cited by 63
Improved single particle localization accuracy with dual objective multifocal plane microscopy
Ram, S., Prabhat, P., Ward, E. S., & Ober, R. J. (2009) · Optics Express · doi:10.1364/oe.17.006881 · Cited by 62
Wang, Y., Quan, T., Zeng, S., & Huang, Z. (2012) · Optics Express · doi:10.1364/oe.20.016039 · Cited by 59
Li, Y., Ishitsuka, Y., Hedde, P. N., & Nienhaus, G. U. (2013) · ACS Nano · doi:10.1021/nn4009388 · Cited by 40
Plasmonics Meets Far-Field Optical Nanoscopy
Balzarotti, F., & Stefani, F. D. (2012) · ACS Nano · doi:10.1021/nn302306m · Cited by 37
Super-resolution surface mapping using the trajectories of molecular probes
Walder, R., Nelson, N., & Schwartz, D. K. (2011) · Nature Communications · doi:10.1038/ncomms1530 · Cited by 34
Fast maximum likelihood algorithm for localization of fluorescent molecules
Starr, R., Stahlheber, S. P., & Small, A. (2012) · Optics Letters · doi:10.1364/ol.37.000413 · Cited by 28
A starter kit for point-localization super-resolution imaging
Manley, S., Gunzenhäuser, J., & Olivier, N. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.10.009 · Cited by 24
Self-citationLocalisation microscopy with quantum dots using non-negative matrix factorisation
Mandula, O., Šestak, I. Š., Heintzmann, R., & Williams, C. K. I. (2014) · Optics Express · doi:10.1364/oe.22.024594 · Cited by 17
SimpleSTORM: a fast, self-calibrating reconstruction algorithm for localization microscopy
Köthe, U., Herrmannsdörfer, F., Kats, I., & Hamprecht, F. A. (2014) · Histochemistry and Cell Biology · doi:10.1007/s00418-014-1211-4 · Cited by 15
Cited by
Super-resolution microscopy with DNA-PAINT
Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F., & Jungmann, R. (2017) · Nature Protocols · doi:10.1038/nprot.2017.024 · Cited by 1,047
SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data
Levet, F., Hosy, E., Kechkar, A., Butler, C., Beghin, A., Choquet, D., & Sibarita, J.-B. (2015) · Nature Methods · doi:10.1038/nmeth.3579 · Cited by 502
Switchable Fluorophores for Single-Molecule Localization Microscopy
Li, H., & Vaughan, J. C. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00767 · Cited by 319
Metrics reloaded: Recommendations for image analysis validation
Maier-Hein, L., Reinke, A., Godau, P., Tizabi, M. D., Buettner, F., Christodoulou, E., Glocker, B., Isensee, F., Kleesiek, J., Kozubek, M., et al. (2022) · arXiv · doi:10.48550/arxiv.2206.01653 · Cited by 59
Essential guidelines for computational method benchmarking
Weber, L. M., Saelens, W., Cannoodt, R., Soneson, C., Hapfelmeier, A., Gardner, P. P., Boulesteix, A.-L., Saeys, Y., & Robinson, M. D. (2019) · Genome Biology · doi:10.1186/s13059-019-1738-8 · Cited by 21
Metadata
- Authors
- Sage, D., Kirshner, H., Pengo, T., Stuurman, N., Min, J., Manley, S., & Unser, M.
- Venue
- Nature Methods
- Published
- 2015-06-15
- Volume
- 12
- Issue
- 8
- Pages
- 717-724
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2125505095
- Cited by
- 396
- References
- 56
- FWCI
- 28.90
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.