.. index:: ! References References ========== Abraham AV, Ram S, Chao J, Ward ES & Ober RJ (2009) Quantitative study of single molecule location techniques. *Optical Express* 17: 23352. Amitai A, Seeber A, Gasser SM & Holcman D (2017) Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories. *Cell reports* 18, 1200-1214. Ankerst M, Breunig MM, Kriegel HP & Sander J (1999) OPTICS: ordering points to identify the clustering structure. *Proceedings of the 1999 ACM SIGMOD international conference on Management of data (SIGMOD '99)* ACM, New York, NY, USA, 49-60. Annibale P, Vanni S, Scarselli M, Rothlisberger U & Radenovic A (2011) Quantitative Photo Activated Localization Microscopy: Unravelling the Effect of Photoblinking. *PLoS ONE* 6(7): e22678. Backlund MP, Joyner R & Moerner WE (2015) Chromosomal locus tracking with proper accounting of static and dynamic errors. *Physical Review* E 91: 062716. Bates M, Huang B, Dempsey GT & Zhuang X (2007) Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes. *Science* 317, 1749. Bates M, Dempsey GT, Chen KH & Zhuang X (2012) Multicolor Super-Resolution Fluorescence Imaging via Multi-Parameter Fluorophore Detection. *ChemPhysChem* 13, 99 – 107. Chao J, Ram S, Ward ES & Ober RJ (2013) Ultrahigh accuracy imaging modality for super-localization microscopy. *Nature Methods* 10, 335-338. Chao J, Ward ES & Ober RJ (2012) Fisher information matrix for branching processes with application to electron-multiplying charge-coupled devices. *Multidimens. Syst. Signal Process*. 23, 349–379. Cisse II, Izeddin I, Causse SZ, Boudarene L, Senecal A, Muresan L, Dugast-Darzacq C, Hajj B, Dahan M & Darzacq X (2013) Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells. s*Science*. 341, 664–667. Coltharp C, Kessler RP & Xiao J (2012) Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements. *PLoS One* 7(12): e51725. Edelstein A, Amodaj N, Hoover K, Vale R & Stuurman N (2010) Computer Control of Microscopes Using μManager. *Current Protocols in Molecular Biology* 14.20.1-14.20.17. Ester M, Kriegel HP, Sander J & Xu X (1996). A density-based algorithm for discovering clusters in large spatial databases with noise. *Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96)* AAAI Press. pp. 226–231. Etheridge TJ, Carr AM & Herbert AD (2022) GDSC SMLM: Single-molecule localisation microscopy software for ImageJ [version 1; peer review: 1 approved]. *Wellcome Open Res* 7:241. Heel M & Schatz M (2005) Fourier shell correlation threshold criteria. *Journal of Structural Biology* 151(3): 250–262. Henriques R, Lelek M, Fornasiero EF, Valtorta F, Zimmer C & Mhlanga MM (2010) QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ. *Nature Methods* 7: 339–340. Hirsch M, Wareham RJ, Martin-Fernandez ML, Hobson MP, Rolfe DJ (2013) A Stochastic Model for Electron Multiplication Charge-Coupled Devices – From Theory to Practice. *PLOS ONE* 8(1): e53671. Holtzer L, Meckel T, Schmidt T (2007) Nanometric three-dimensional tracking of individual quantum dots in cells. *Appl. Phys. Lett*. 90: 053902. Hozé NHD (2017) Statistical methods for large ensembles of super-resolution stochastic single particle trajectories in cell biology. *Annual Review of Statistics and Its Application* 4, 189-223. Huang F, Hartwich T, Rivera-Molina FE *et al* (2013) Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithms. *Nature Methods* 10: 653–658. Hurvich CM & Tsai CL (1989) Regression and time series model selection in small samples. *Biometrika* 76: 297–307. Izeddin I, Récamier V, Bosanac L Cissé II, Boudarene L, Dugast-Darzacq C Proux F, Bénichou O, Voituriez R, Bensaude O, Dahan M & Darzacq X (2014) Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus. *eLife* e02230. Kriegel HP, Kröger P, Schubert E & Zimek A (2009) LoOP: local outlier probabilities. *Proceedings of the 18th ACM conference on Information and knowledge management (CIKM '09)* ACM, New York, NY, USA, 1649-1652. Laurence TA & Chromy BA (2010) Efficient maximum likelihood estimator fitting of histograms. *Nature Methods* 7: 338-339. Lin R, Clowsley AH, Jayasinghe ID, Baddeley D & Soeller C (2017) Algorithmic corrections for localization microscopy with sCMOS cameras - characterisation of a computationally efficient localization approach. *Optical Express* 25(10): 11701-11716. Moreira and Santos (2007) Concave hull: A k-nearest neighbours approach for the computation of the region occupied by a set of points. * Conference: GRAPP 2007*, Proceedings of the Second International Conference on Computer Graphics Theory and Applications, Barcelona, Spain. Mortensen KI, Churchman LS, Spudich JA & Flyvbjerg H (2010) Optimized localization analysis for single-molecule tracking and super-resolution microscopy. *Nature Methods* 7(5): 377-81. Neubeck A & Van Gool L (2006) Efficient Non-Maximum Suppression. *Pattern Recognition, 2006. ICPR 2006. 18th International Conference on* vol.3: 850-855 Nieuwenhuizen RPJ, Lidke KA, Bates M, Puig DL, Grunwald D, Stallinga S & Rieger B (2013) Measuring image resolution in optical nanoscopy. *Nature Methods* 10: 557. Park JS & Oh SJ (2012) A New Concave Hull Algorithm and Concaveness Measure for n-dimensional Datasets. *Journal of Information Science and Engineering* 28:587-600. Press WH, Teukolsky S, Vetterling W, Flannery B (2002) Numerical Recipes in C++: The Art of Scientific Computing. *Cambridge University Press*, 2nd edition. Puchnar EM, Walter JM, Kasper R, Huang B & Lim WA (2013) Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory. *PNAS* 110: 16015-16020. Rousseeuw P & Leroy A (1987) Robust Regression and Outlier Detection. New York: Wiley Schneider CA, Rasband WS & Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. *Nature Methods* 9: 671-675. Schneider J, & Vlachos M (2013) Fast parameterless density-based clustering via random projections. *Proceedings of the 22nd ACM international conference on Conference on information & knowledge management (CIKM '13)* ACM, New York, NY, USA, 861-866. Sengupta P, Jovanovic-Talisman T & Lippincott-Schwartz J (2013) Quantifying spatial resolution in point-localisation super-resolution images using pair correlation analysis. *Nature Protocols* 8: 345-354. Sengupta P, Jovanovic-Talisman T, Skoko D, Renz M, Veatch SL & Lippincott-Schwartz J (2011) Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. *Nature Methods* 8: 969-975. Sergé A, Bertaux N, Rigneault H & Marguet D (2008) Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes. *Nature Methods* 5: 687-694. Snyder DL, Helstrom CW, Lanterman AD, Faisal M & White RL (1995) Compensation for readout noise in CCD images. *Journal of the Optical Society of America* 12: 272-283. Smith CS, Joseph N, Rieger B, Lidke KA (2010) Fast, single-molecule localization that achieves theoretically minimum uncertainty. *Nature Methods* 7: 373-375. Stetson PB (1987) DAOPHOT: A compute program for crowded-field stellar photometry. *Publ Astrom Soc Pac* 99: 191-222. Tubbs RN (2004) Lucky exposures: Diffraction limited astronomical imaging through the atmosphere. *Observatory* 124. Ulbrich MH & Isacoff EY (2007) Subunit counting in membrane-bound proteins. *Nature Methods* 4: 319-321. Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ & Kapanidis AN (2013) Single-molecule DNA repair in live bacteria. *PNAS* 110: 8063-8068. Veatch SL, Machta BB, Shelby SA, Chiang EN, Holowka DA & Baird BA (2012) Correlation Functions Quantify Super-Resolution Images and Estimate Apparent Clustering Due to Over-Counting. *PLoS One* 7(2): e31457. Weimann L, Ganzinger KA, McColl J, Irvine KL, Davis SJ, Gay NJ, Bryant CE & Klenerman D (2013) A Quantitative Comparison of Single-Dye Tracking Analysis Tools Using Monte Carlo Simulations. *PLoS One* 8(5): e64287. Wolter S, Schüttpelz M, Tscherepanow M, Van De Linde S, Heilemann M & Sauer M (2010) Real-time computation of subdiffraction-resolution fluorescence images. *Journal of Microscopy* 237: 12–22.