L. Andronov, ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy, Sci. Rep, 2016.

D. Baddeley, Visualization of Localization Microscopy Data, Microsc. Microanal, vol.16, pp.64-72, 2010.

N. Banterle, Fourier ring correlation as a resolution criterion for super-resolution microscopy, J. Struct. Biol, vol.183, pp.363-367, 2013.

H. Deschout, Precisely and accurately localizing single emitters in fluorescence microscopy, Nat. Methods, vol.11, pp.253-266, 2014.

A. D. Edelstein, Advanced methods of microscope control using lManager software, J. Biol. Methods, vol.1, p.10, 2014.

M. El-beheiry and M. Dahan, ViSP: representing single-particle localizations in three dimensions, Nat. Methods, vol.10, pp.689-690, 2013.

M. Erdelyi, Correcting chromatic offset in multicolor superresolution localization microscopy, Opt. Express, vol.21, pp.10978-10988, 2013.

R. Henriques, QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ, Nat. Methods, vol.7, pp.339-340, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02081312

B. Huang, Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy, Science, vol.319, pp.810-813, 2008.

C. Lemaître, Nuclear position dictates DNA repair pathway choice, Genes Dev, vol.28, pp.2450-2463, 2014.

F. Levet, SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data, Nat. Methods, vol.12, pp.1065-1071, 2015.

M. J. Mlodzianoski, Sample drift correction in 3D fluorescence photoactivation localization microscopy, Opt. Express, vol.19, pp.15009-15019, 2011.

R. P. Nieuwenhuizen, Measuring image resolution in optical nanoscopy, Nat. Methods, vol.10, pp.557-562, 2013.

M. Ovesn-y, ThunderSTORM: a comprehensive ImageJ Plug-in for PALM and STORM data analysis and super-resolution imaging, Bioinformatics, vol.30, pp.2389-2390, 2014.

D. M. Owen, PALM imaging and cluster analysis of protein heterogeneity at the cell surface, J. Biophoton, vol.3, pp.446-454, 2010.

T. Pengo, PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy, Bioinformatics, vol.31, pp.797-798, 2015.

E. J. Rees, Quantitative evaluation of software packages for singlemolecule localization microscopy, Nat. Methods, vol.15, pp.717-724, 2013.

A. Small and S. Stahlheber, Fluorophore localization algorithms for super-resolution microscopy, Nat. Methods, vol.11, pp.267-279, 2014.

S. Wolter, rapidSTORM: accurate, fast open-source software for localization microscopy, Nat. Methods, vol.9, pp.1040-1041, 2012.

L. Andronov, ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy, Sci. Rep, 2016.

E. Abbe, Beiträge zur Theorie des Mikroskops und der mikroskopischen Wahrnehmung, Arch. Mikrosk. Anat, vol.9, pp.413-468, 1873.

D. Baddeley, Visualization of Localization Microscopy Data, Microsc. Microanal, vol.16, pp.64-72, 2010.

N. Banterle, Fourier ring correlation as a resolution criterion for super-resolution microscopy, J. Struct. Biol, vol.183, pp.363-367, 2013.

M. Born and E. Wolf, Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light, pp.461-475, 1999.

W. S. Cleveland, Robust Locally Weighted Regression and Smoothing Scatterplots, J. Am, 1979.

, Stat. Assoc, vol.74, pp.829-836

B. Delaunay, Sur la sphère vide. A la mémoire de Georges Voronoï, B. Acad. Sci. URSS, vol.6, pp.793-800, 1934.

H. Deschout, Precisely and accurately localizing single emitters in fluorescence microscopy, Nat. Methods, vol.11, pp.253-266, 2014.

A. D. Edelstein, Advanced methods of microscope control using ?Manager software, 2014.

, J. Biol. Methods, vol.1, p.10

A. Egner and S. W. Hell, Aberrations in confocal and multi-photon fluorescence microscopy induced by refractive index mismatch, Handbook of Biological Confocal Microscopy, pp.404-413, 2006.

U. Endesfelder and M. Heilemann, Art and artifacts in single-molecule localization microscopy: beyond attractive images, Nat. Methods, vol.11, pp.235-238, 2014.

M. El-beheiry and M. Dahan, ViSP: representing single-particle localizations in three dimensions, Nat. Methods, vol.10, pp.689-690, 2013.

M. Guizar-sicairos, S. T. Thurman, and J. R. Fienup, Efficient subpixel image registration algorithms, Opt. Lett, vol.33, pp.156-158, 2008.

R. Henriques, QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ, Nat. Methods, vol.7, pp.339-340, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02081312

B. Huang, Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy, Science, vol.319, pp.810-813, 2008.

M. F. Juette, Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples, Nat. Methods, vol.5, pp.527-529, 2008.

R. P. Nieuwenhuizen, Measuring image resolution in optical nanoscopy, Nat. Methods, vol.10, pp.557-562, 2013.

R. J. Ober, Localization Accuracy in Single-Molecule Microscopy, Biophys. J, vol.86, pp.1185-1200, 2004.

M. Ovesný, ThunderSTORM: A Comprehensive ImageJ Plug-in for PALM and STORM Data Analysis and Super-Resolution Imaging, Bioinformatics, vol.30, pp.2389-90, 2014.

S. R. Pavani, Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function, Proc. Natl. Acad. Sci. USA, vol.106, pp.2995-2999, 2009.

T. Pengo, PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy, Bioinformatics, vol.31, pp.797-798, 2015.

E. J. Rees, Elements of image processing in localization microscopy, J. Opt, vol.15, p.94012, 2013.

B. Rieger and S. Stallinga, The Lateral and Axial Localization Uncertainty in Super-Resolution Light Microscopy, ChemPhysChem, vol.15, pp.664-670, 2014.

R. Sibson, A Brief Description of Natural Neighbour Interpolation, 1981.

, Interpreting Multivariate Data, pp.21-36

A. R. Smith, Color gamut transform pairs, Comp. Graph, vol.12, pp.12-19, 1978.

A. Szymborska, Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging, Science, vol.341, pp.655-658, 2013.

M. Van-heel, A new generation of the IMAGIC image processing system, J. Struct. Biol, vol.116, pp.17-24, 1996.

G. Voronoi, Nouvelles applications des paramètres continus à la théorie des formes quadratiques, J. Reine Angew. Math, vol.133, pp.97-178, 1908.

S. Wolter, rapidSTORM: accurate, fast open-source software for localization microscopy, Nat. Methods, vol.9, pp.1040-1041, 2012.

A. Szymborska, Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging, Science, vol.341, pp.655-658, 2013.

N. Banterle, H. B. Khanh, E. A. Lemke, and M. Beck, Fourier ring correlation as a resolution criterion for super-resolution microscopy, J. Struct. Biol, vol.183, pp.363-367, 2013.

R. P. Nieuwenhuizen, Measuring image resolution in optical nanoscopy, Nat. Methods, vol.10, pp.557-562, 2013.

D. Baddeley, M. B. Cannell, and C. Soeller, Visualization of Localization Microscopy Data, Microsc. Microanal, vol.16, pp.64-72, 2010.

Y. Wang, Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm, Opt. Express, vol.22, pp.15982-15991, 2014.

S. Malkusch, Coordinate-based colocalization analysis of single-molecule localization microscopy data, Histochem. Cell Biol, vol.137, pp.1-10, 2012.

J. Rossy, E. Cohen, K. Gaus, and D. M. Owen, Method for co-cluster analysis in multichannel single-molecule localisation data, Histochem. Cell Biol, vol.141, pp.605-612, 2014.

, Scientific RepoRts |, vol.6

M. A. Ricci, C. Manzo, M. F. Garc?a-parajo, M. Lakadamyali, and M. P. Cosma, Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes in Vivo, Cell, vol.160, pp.1145-1158, 2015.

N. Ehmann, Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states, Nat. Commun, vol.5, p.4650, 2014.

S. V. Pageon, Superresolution Microscopy Reveals Nanometer-Scale Reorganization of Inhibitory Natural Killer Cell Receptors upon Activation of NKG2D, Sci. Signal, vol.6, p.62, 2013.

J. Gao, Mechanistic insights into EGFR membrane clustering revealed by super-resolution imaging, Nanoscale, vol.7, pp.2511-2519, 2015.

S. L. Veatch, Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting, Plos One, vol.7, p.31457, 2012.

P. Sengupta, Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis, Nat. Methods, vol.8, pp.969-975, 2011.

C. Lemaître, Nuclear position dictates DNA repair pathway choice, Gene. Dev, vol.28, pp.2450-2463, 2014.

M. Ester, H. Kriegel, S. Jörg, and X. Xu, A density-based algorithm for discovering clusters in large spatial databases with noise, Paper presented at Second International Conference on Knowledge Discovery and Data Mining, 1996.

P. Rubin-delanchy, Bayesian cluster identification in single-molecule localization microscopy data, Nat. Methods, vol.12, pp.1072-1076, 2015.

F. Levet, SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data, Nat. Methods, vol.12, pp.1065-1071, 2015.

G. Voronoi, Nouvelles applications des paramètres continus à la théorie des formes quadratiques, J. Reine Angew. Math, vol.133, pp.97-178, 1908.

F. Aurenhammer, Voronoi Diagrams -A Survey of a Fundamental Geometric Data Structure, ACM Comput. Surv, vol.23, pp.345-405, 1991.

P. Felfer, A. Ceguerra, S. Ringer, and J. Cairney, Detecting and extracting clusters in atom probe data: A simple, automated method using Voronoi cells, Ultramicroscopy, vol.150, pp.30-36, 2015.

A. Egner and S. W. Hell, Aberrations in confocal and multi-photon fluorescence microscopy induced by refractive index mismatch in Handbook of Biological Confocal Microscopy, pp.404-412, 2006.

E. Betzig, Imaging Intracellular Fluorescent Proteins at Nanometer Resolution, Science, vol.313, pp.1642-1645, 2006.

N. Ahuja, Dot pattern processing using Voronoi Neighborhoods, IEEE T. Pattern Anal. PAMI-4, pp.336-343, 1982.

G. G. Maul, Nuclear pore complexes. Elimination and reconstruction during mitosis, J. Cell Biol, vol.74, pp.492-500, 1977.

M. Winey, D. Yarar, J. Giddings, H. , T. Mastronarde et al., Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes, Mol. Biol. Cell, vol.8, pp.2119-2132, 1997.

B. W. Baer and D. Rhodes, Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes, Nature, vol.301, pp.482-488, 1983.

L. Louters and R. Chalkley, Exchange of histones H1, H2A, and H2B in vivo, Biochemistry, vol.24, pp.3080-3085, 1985.

A. Hamiche, Interaction of the histone (H3-H4)2 tetramer of the nucleosome with positively supercoiled DNA minicircles: Potential flipping of the protein from a left-to a right-handed superhelical form, Proc. Natl. Acad. Sci. USA, vol.93, pp.7588-7593, 1996.
URL : https://hal.archives-ouvertes.fr/hal-02328381

D. Reem, The geometric stability of Voronoi diagrams with respect to small changes of the sites, Paper presented at 27th Annual ACM Symposium on Computational Geometry (SoCG), pp.13-15, 2011.

L. Andronov, Y. Lutz, J. Vonesch, and B. P. Klaholz, SharpViSu: integrated analysis and segmentation of super-resolution microscopy data, Bioinformatics, 2016.

N. Olivier, D. Keller, V. S. Rajan, P. Gönczy, and S. Manley, Simple buffers for 3D STORM microscopy, Biomed. Opt. Express, vol.4, pp.885-899, 2013.

R. Sibson, A brief description of natural neighbour interpolation in Interpreting multivariate data, pp.21-36, 1981.

M. Van-heel, G. Harauz, and E. V. Orlova, A new generation of the IMAGIC image processing system, J. Struct. Biol, vol.116, pp.17-24, 1996.

L. Andronov and I. Orlov, ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy, Sci. Rep, vol.6, p.24084, 2016.

L. Andronov and Y. Lutz, SharpViSu: integrated analysis and segmentation of super-resolution microscopy data, Bioinformatics, vol.32, pp.2239-2241, 2016.

D. Aquino, Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores, Nat. Methods, vol.8, pp.353-359, 2011.

J. Arnold, Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy, Biophys. J, vol.110, pp.860-869, 2016.

F. Aurenhammer, Voronoi Diagrams-a Survey of a Fundamental Geometric Data Structure, ACM Comput Surv, vol.23, pp.345-405, 1991.

D. Baddeley, Visualization of Localization Microscopy Data, Microsc. Microanal, vol.16, pp.64-72, 2010.

C. B. Barber, The Quickhull algorithm for convex hulls, Acm Trans. Math. Softw, vol.22, pp.469-483, 1996.

L. Barna, Correlated confocal and super-resolution imaging by Vivid-STORM, Nat. Protoc, vol.11, pp.163-183, 2016.

M. E. Beheiry and M. Dahan, ViSP: representing single-particle localizations in three dimensions, Nat. Methods, vol.10, pp.689-690, 2013.

E. Betzig, Imaging Intracellular Fluorescent Proteins at Nanometer Resolution, Science, vol.313, pp.1642-1645, 2006.

M. Ester, A density-based algorithm for discovering clusters in large spatial databases with noise, pp.226-231, 1996.

J. Fölling, Fluorescence nanoscopy by ground-state depletion and single-molecule return, Nat. Methods, vol.5, pp.943-945, 2008.

C. Franke, Photometry unlocks 3D information from 2D localization microscopy data, Nat. Methods, vol.14, pp.41-44, 2017.

T. Fukagawa and W. C. Earnshaw, The Centromere: Chromatin Foundation for the Kinetochore Machinery, Dev. Cell, vol.30, pp.496-508, 2014.

B. Huang, Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy, Science, vol.319, pp.810-813, 2008.

E. Jones, SciPy: Open source scientific tools for Python, 2001.

M. F. Juette, Three-dimensional sub-100 nm resolution fluorescence microscopy of thick samples, Nat. Methods, vol.5, pp.527-529, 2008.

M. A. Karreman, Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy, J Cell Sci, vol.129, pp.444-456, 2016.

R. I. Koning, Correlative cryo-fluorescence light microscopy and cryoelectron tomography of Streptomyces, Methods Cell Biol, vol.124, pp.217-239, 2014.

A. Lampe, Multi-colour direct STORM with red emitting carbocyanines, Biol. Cell, vol.104, pp.229-237, 2012.

F. Levet, SR-Tesseler: a method to segment and quantify localizationbased super-resolution microscopy data, Nat. Methods, vol.12, pp.1065-1071, 2015.

Y. Li, Fast, robust and precise 3D localization for arbitrary point spread functions. bioRxiv, 172643, Histochem. Cell Biol, vol.137, pp.1-10, 2012.

N. Olivier, Simple buffers for 3D STORM microscopy, Biomed. Opt. Express, vol.4, pp.885-899, 2013.

I. Orlov, The integrative role of cryo electron microscopy in molecular and cellular structural biology, Biol. Cell, vol.109, pp.81-93, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-02409721

D. M. Owen, Quantitative Analysis of Three-Dimensional Fluorescence Localization Microscopy Data, Biophys. J, vol.105, pp.5-07, 2013.

S. V. Pageon, Clus-DoC: A combined cluster detection and colocalization analysis for single-molecule localization microscopy data, Mol. Biol. Cell, 2016.

D. K. Palmer, A 17-kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones, J. Cell Biol, vol.104, pp.805-815, 1987.

S. R. Pavani, Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function, Proc. Natl. Acad. Sci, vol.106, pp.2995-2999, 2009.

E. F. Pettersen, UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem, vol.25, pp.1605-1612, 2004.

P. Ramachandran and G. Varoquaux, Mayavi: 3D Visualization of Scientific Data, Comput. Sci. Eng, vol.13, pp.40-51, 2011.
URL : https://hal.archives-ouvertes.fr/inria-00528985

M. A. Ricci, Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo, Cell, vol.160, pp.1145-1158, 2015.

J. Rossy, Method for co-cluster analysis in multichannel singlemolecule localisation data, Histochem. Cell Biol, vol.141, pp.605-612, 2014.

P. Rubin-delanchy, Bayesian cluster identification in single-molecule localization microscopy data, Nat. Methods, vol.12, pp.1072-1076, 2015.

R. T. Schirra and P. Zhang, Correlative fluorescence and electron microscopy, Curr. Protoc. Cytom, vol.70, pp.12-36, 2014.

M. Schorb, New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography, J. Struct. Biol, vol.197, pp.83-93, 2017.

M. Shuaib, HJURP binds CENP-A via a highly conserved N-terminal domain and mediates its deposition at centromeres, Proc. Natl. Acad. Sci, vol.107, pp.1349-1354, 2010.

R. Sibson, A brief description of natural neighbour interpolation, Barnet,V, pp.21-35, 1981.

R. E. Thompson, Precise nanometer localization analysis for individual fluorescent probes, Biophys. J, vol.82, pp.2775-2783, 2002.

S. Walt and . Van-der, The NumPy Array: A Structure for Efficient Numerical Computation, Comput. Sci. Eng, vol.13, pp.22-30, 2011.
URL : https://hal.archives-ouvertes.fr/inria-00564007

D. J. Williamson, Pre-existing clusters of the adaptor Lat do not participate in early T cell signaling events, Nat. Immunol, vol.12, pp.655-662, 2011.

P. Winckler, Identification and super-resolution imaging of ligandactivated receptor dimers in live cells, Sci. Rep, vol.3, p.2387, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00909281

G. Wolff, Towards correlative super-resolution fluorescence and electron cryo-microscopy, Biol. Cell, vol.108, pp.245-258, 2016.

E. Abbe, Ueber einen neuen Beleuchtungsapparat am Mikroskop, Arch. Für Mikrosk. Anat, vol.9, pp.469-480, 1873.

A. V. Abraham, S. Ram, J. Chao, E. S. Ward, and R. J. Ober, Quantitative study of single molecule location estimation techniques, Opt. Express, vol.17, pp.23352-23373, 2009.

F. Aguet, D. V. Ville, and M. Unser, A maximum-likelihood formalism for subresolution axial localization of fluorescent nanoparticles, Opt. Express, vol.13, pp.10503-10522, 2005.

G. B. Airy, On the Diffraction of an Object-glass with Circular Aperture, Trans. Camb. Philos. Soc, vol.5, p.283, 1835.

J. R. Allen, S. T. Ross, and M. W. Davidson, Single molecule localization microscopy for superresolution, J. Opt, vol.15, p.94001, 2013.

E. J. Ambrose, A Surface Contact Microscope for the study of Cell Movements, Nature, vol.178, pp.1194-1194, 1956.

W. P. Ambrose, T. Basché, and W. E. Moerner, Detection and spectroscopy of single pentacene molecules in a p-terphenyl crystal by means of fluorescence excitation, J. Chem. Phys, vol.95, pp.7150-7163, 1991.

W. P. Ambrose, P. M. Goodwin, and J. P. Nolan, Single-molecule detection with total internal reflection excitation: Comparing signal-to-background and total signals in different geometries, Cytometry, vol.36, pp.224-231, 1999.

R. Ando, H. Hama, M. Yamamoto-hino, H. Mizuno, and A. Miyawaki, An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein, Proc. Natl. Acad. Sci, vol.99, pp.12651-12656, 2002.

R. Ando, H. Mizuno, and A. Miyawaki, Regulated Fast Nucleocytoplasmic Shuttling Observed by Reversible Protein Highlighting, Science, vol.306, pp.1370-1373, 2004.

L. Andronov, Y. Lutz, J. Vonesch, and B. P. Klaholz, SharpViSu: integrated analysis and segmentation of super-resolution microscopy data, Bioinformatics, vol.32, pp.2239-2241, 2016.

L. Andronov, I. Orlov, Y. Lutz, J. Vonesch, and B. P. Klaholz, ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy, Sci. Rep, vol.6, p.24084, 2016.

L. Andronov, J. Michalon, K. Ouararhni, I. Orlov, A. Hamiche et al., 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-02409748

D. Aquino, A. Schönle, C. Geisler, C. Middendorff, C. A. Wurm et al., Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores, Nat. Methods, vol.8, pp.353-359, 2011.

E. Auksorius, B. R. Boruah, C. Dunsby, P. M. Lanigan, G. Kennedy et al., , 2008.

D. Axelrod, Cell-substrate contacts illuminated by total internal reflection fluorescence, J. Cell Biol, vol.89, pp.141-145, 1981.

M. P. Backlund, M. D. Lew, A. S. Backer, S. J. Sahl, and W. E. Moerner, The Role of, 2014.

, Molecular Dipole Orientation in Single-Molecule Fluorescence Microscopy and Implications for Super-Resolution Imaging, ChemPhysChem, vol.15, pp.587-599

D. Baddeley, M. B. Cannell, and C. Soeller, Visualization of Localization Microscopy Data, Microsc. Microanal, vol.16, pp.64-72, 2010.

N. Banterle, K. H. Bui, E. A. Lemke, and M. Beck, Fourier ring correlation as a resolution criterion for super-resolution microscopy, J. Struct. Biol, vol.183, pp.363-367, 2013.

J. Bär, O. Kobler, B. Bommel, and M. Mikhaylova, Periodic F-actin structures shape the neck of dendritic spines, Sci. Rep, vol.6, p.37136, 2016.

M. V. Baranov, N. H. Revelo, I. Dingjan, R. Maraspini, M. Beest et al., SWAP70 Organizes the Actin Cytoskeleton and Is Essential for Phagocytosis, Cell Rep, vol.17, pp.1518-1531, 2016.

B. Barlag, O. Beutel, D. Janning, F. Czarniak, C. P. Richter et al., Single molecule super-resolution imaging of proteins in living Salmonella enterica using self-labelling enzymes, Sci. Rep, vol.6, p.31601, 2016.

M. Bates, T. R. Blosser, and X. Zhuang, Short-Range Spectroscopic Ruler Based on a Single-Molecule Optical Switch, Phys. Rev. Lett, vol.94, p.108101, 2005.

M. Bates, B. Huang, G. T. Dempsey, and X. Zhuang, Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes, Science, vol.317, pp.1749-1753, 2007.

F. Baumgart, A. M. Arnold, K. Leskovar, K. Staszek, M. Fölser et al., Varying label density allows artifact-free analysis of membraneprotein nanoclusters, Nat. Methods, vol.13, pp.661-664, 2016.

J. Bednar, I. Garcia-saez, R. Boopathi, A. R. Cutter, G. Papai et al., Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1, Mol. Cell, vol.66, pp.384-397, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01537811

F. Bergermann, L. Alber, S. J. Sahl, J. Engelhardt, and S. W. Hell, 2000-fold parallelized dual-color STED fluorescence nanoscopy, Opt. Express, vol.23, pp.211-223, 2015.

J. Besag and P. J. Diggle, Simple Monte Carlo Tests for Spatial Pattern, J. R. Stat. Soc. Ser. C Appl. Stat, vol.26, pp.327-333, 1977.

P. Bethge, R. Chéreau, E. Avignone, G. Marsicano, and U. V. Nägerl, Two-Photon Excitation STED Microscopy in Two Colors in Acute Brain Slices, Biophys. J, vol.104, pp.778-785, 2013.

E. Betzig, Proposed method for molecular optical imaging, Opt. Lett, vol.20, pp.237-239, 1995.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych et al., Imaging Intracellular Fluorescent Proteins at Nanometer Resolution, Science, vol.313, pp.1642-1645, 2006.

J. Bewersdorf, R. Schmidt, and S. W. Hell, Comparison of I5M and 4Pi-microscopy, 2006.

, J. Microsc, vol.222, pp.105-117

N. Bielopolski, A. D. Lam, D. Bar-on, M. Sauer, E. L. Stuenkel et al., , 2014.

, Differential Interaction of Tomosyn with Syntaxin and SNAP25 Depends on Domains in the WD40 ?-Propeller Core and Determines Its Inhibitory Activity, J. Biol. Chem, vol.289, pp.17087-17099

B. E. Black, L. E. Jansen, P. S. Maddox, D. R. Foltz, A. B. Desai et al., Centromere Identity Maintained by Nucleosomes Assembled with Histone H3 Containing the CENP-A Targeting Domain, Mol. Cell, vol.25, pp.309-322, 2007.

M. D. Blower, B. A. Sullivan, and G. H. Karpen, Conserved Organization of Centromeric Chromatin in Flies and Humans, Dev. Cell, vol.2, pp.319-330, 2002.

H. Bock, C. Geisler, C. A. Wurm, C. Middendorff, S. Jakobs et al., Two-color far-field fluorescence nanoscopy based on photoswitchable emitters, Appl. Phys. B, vol.88, pp.161-165, 2007.

D. L. Bodor, L. P. Valente, J. F. Mata, B. E. Black, and L. E. Jansen, Assembly in G1 phase and long-term stability are unique intrinsic features of CENP-A nucleosomes, Mol. Biol. Cell, vol.24, pp.923-932, 2013.

D. L. Bodor, J. F. Mata, M. Sergeev, A. F. David, K. J. Salimian et al., The quantitative architecture of centromeric chromatin, vol.3, p.2137, 2014.

R. Boettcher, S. M. Haig, and W. C. Bridges, Behavioral Patterns and Nearest Neighbor Distances among Nonbreeding American Avocets, The Condor, vol.96, pp.973-986, 1994.

A. N. Boettiger, B. Bintu, J. R. Moffitt, S. Wang, B. J. Beliveau et al., Super-resolution imaging reveals distinct chromatin folding for different epigenetic states, Nature, vol.529, pp.418-422, 2016.

M. Bohn, P. Diesinger, R. Kaufmann, Y. Weiland, P. Müller et al., Localization Microscopy Reveals Expression-Dependent Parameters of Chromatin Nanostructure, Biophys. J, vol.99, pp.1358-1367, 2010.

M. Bossi, J. Fölling, V. N. Belov, V. P. Boyarskiy, R. Medda et al., Multicolor Far-Field Fluorescence Nanoscopy through Isolated Detection of Distinct Molecular Species, Nano Lett, vol.8, pp.2463-2468, 2008.

S. Bretschneider, C. Eggeling, and S. W. Hell, Breaking the Diffraction Barrier in Fluorescence Microscopy by Optical Shelving, Phys. Rev. Lett, vol.98, p.218103, 2007.

E. M. Brumberg and T. N. Krylova, Primenenie interferentsionnykh delitelnykh zerkal v fluorestsentnoi mikroskopii, Zh Obshch Biol, vol.14, pp.461-464, 1953.

J. Bückers, D. Wildanger, G. Vicidomini, L. Kastrup, and S. W. Hell, Simultaneous multi-lifetime multi-color STED imaging for colocalization analyses, Opt. Express, vol.19, pp.3130-3143, 2011.

M. Bui, E. K. Dimitriadis, C. Hoischen, E. An, D. Quénet et al., Cell-Cycle-Dependent Structural Transitions in the Human CENP-A Nucleosome In Vivo, Cell, vol.150, pp.317-326, 2012.

J. S. Burmeister, L. A. Olivier, W. M. Reichert, and G. A. Truskey, Application of total internal reflection fluorescence microscopy to study cell adhesion to biomaterials, Biomaterials, vol.19, pp.307-325, 1998.

D. H. Burns, J. B. Callis, G. D. Christian, and E. R. Davidson, Strategies for attaining superresolution using spectroscopic data as constraints, Appl. Opt, vol.24, pp.154-161, 1985.

C. W. Carroll, K. J. Milks, and A. F. Straight, Dual recognition of CENP-A nucleosomes is required for centromere assembly, J. Cell Biol, vol.189, pp.1143-1155, 2010.

A. R. Carter, G. M. King, T. A. Ulrich, W. Halsey, D. Alchenberger et al.,

M. A. Castro, . De, C. Höbartner, and F. Opazo, Aptamers provide superior stainings of cellular receptors studied under super-resolution microscopy, PLOS ONE, vol.12, 2017.

M. K. Cheezum, W. F. Walker, and W. H. Guilford, Quantitative Comparison of Algorithms for Tracking Single Fluorescent Particles, Biophys. J, vol.81, pp.2378-2388, 2001.

J. Chen, J. Gao, M. Zhang, M. Cai, H. Xu et al., , 2016.

, Systemic localization of seven major types of carbohydrates on cell membranes by dSTORM imaging, Sci. Rep, vol.6, p.30247

R. Chéreau, G. E. Saraceno, J. Angibaud, D. Cattaert, and U. V. Nägerl, , 2017.

, Superresolution imaging reveals activity-dependent plasticity of axon morphology linked to changes in action potential conduction velocity, Proc. Natl. Acad. Sci, vol.114, pp.1401-1406

J. Choi, K. , and D. , Notch spatial filtering of image artifacts for structured illumination microscopy of cell-based assays, Opt. Commun, vol.308, pp.142-146, 2013.

C. K. Choi, M. Vicente-manzanares, J. Zareno, L. A. Whitmore, A. Mogilner et al., Actin and alpha-actinin orchestrate the assembly and maturation of nascent adhesions in a myosin II motor-independent manner, Nat. Cell Biol, vol.10, pp.1039-1075, 2008.

D. M. Chudakov, V. V. Belousov, A. G. Zaraisky, V. V. Novoselov, D. B. Staroverov et al., Kindling fluorescent proteins for precise in vivo photolabeling, Nat. Biotechnol, vol.21, pp.191-194, 2003.

L. S. Churchman, Z. Ökten, R. S. Rock, J. F. Dawson, and J. A. Spudich, Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time, Proc. Natl. Acad. Sci. U. S. A, vol.102, pp.1419-1423, 2005.

P. J. Clark and F. C. Evans, , 1954.

C. Coltharp, X. Yang, X. , and J. , Quantitative analysis of single-molecule superresolution images, Curr. Opin. Struct. Biol, vol.28, pp.112-121, 2014.

T. Cordes, M. Strackharn, S. W. Stahl, W. Summerer, C. Steinhauer et al., Resolving Single-Molecule Assembled Patterns with Superresolution Blink-Microscopy, Nano Lett, vol.10, pp.645-651, 2010.

Y. Dalal, H. Wang, S. Lindsay, and S. Henikoff, Tetrameric Structure of, 2007.

, Centromeric Nucleosomes in Interphase Drosophila Cells, PLOS Biol, vol.5, p.218

J. G. Danzl, S. C. Sidenstein, C. Gregor, N. T. Urban, P. Ilgen et al.,

, Coordinate-targeted fluorescence nanoscopy with multiple off states, Nat. Photonics, vol.10, pp.122-128

P. Davidovits and M. D. Egger, Scanning Laser Microscope for Biological Investigations, Appl. Opt, vol.10, pp.1615-1619, 1971.

G. T. Dempsey, J. C. Vaughan, K. H. Chen, M. Bates, and X. Zhuang, Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging, Nat. Methods, vol.8, pp.1027-1036, 2011.

H. Deschout, F. C. Zanacchi, M. Mlodzianoski, A. Diaspro, J. Bewersdorf et al., Precisely and accurately localizing single emitters in fluorescence microscopy, Nat. Methods, vol.11, pp.253-266, 2014.

E. D'este, D. Kamin, F. Balzarotti, and S. W. Hell, Ultrastructural anatomy of nodes of Ranvier in the peripheral nervous system as revealed by STED microscopy, Proc. Natl. Acad. Sci, vol.114, pp.191-199, 2017.

R. M. Dickson, A. B. Cubitt, R. Y. Tsien, and W. E. Moerner, On/off blinking and switching behaviour of single molecules of green fluorescent protein, Nature, vol.388, pp.355-358, 1997.

L. T. Díez, C. Bönsch, S. Malkusch, Z. Truan, M. Munteanu et al., Coordinate-based co-localization-mediated analysis of arrestin clustering upon stimulation of the C-C chemokine receptor 5 with RANTES/CCL5 analogues, Histochem. Cell Biol, vol.142, pp.69-77, 2014.

E. K. Dimitriadis, C. Weber, R. K. Gill, S. Diekmann, and Y. Dalal, Tetrameric organization of vertebrate centromeric nucleosomes, Proc. Natl. Acad. Sci, vol.107, pp.20317-20322, 2010.

G. L. Dirichlet, Über die Reduction der positiven quadratischen Formen mit drei unbestimmten ganzen Zahlen, J. Für Reine Angew. Math, vol.40, pp.209-227, 1850.

P. Dixon, Ripley's K function, Encycl. Environmetrics, pp.1796-1803, 2001.

E. M. Dunleavy, D. Roche, H. Tagami, N. Lacoste, D. Ray-gallet et al., HJURP Is a Cell-Cycle-Dependent Maintenance and Deposition Factor of CENP-A at Centromeres, Cell, vol.137, pp.485-497, 2009.

E. M. Dunleavy, G. Almouzni, and G. H. Karpen, H3.3 is deposited at centromeres in S phase as a placeholder for newly assembled CENP-A in G1 phase, Nucleus, vol.2, pp.146-157, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00742956

E. M. Dunleavy, W. Zhang, and G. H. Karpen, Solo or doppio: how many CENP-As make a centromeric nucleosome?, Nat. Struct. Mol. Biol, vol.20, pp.648-650, 2013.

K. W. Dunn, M. M. Kamocka, and J. H. Mcdonald, A practical guide to evaluating colocalization in biological microscopy, Am. J. Physiol. -Cell Physiol, vol.300, pp.723-742, 2011.

C. Eggeling, C. Ringemann, R. Medda, G. Schwarzmann, K. Sandhoff et al.,

V. N. Belov, B. Hein, C. Von-middendorff, and A. Schönle, Direct observation of the nanoscale dynamics of membrane lipids in a living cell, Nature, vol.457, pp.1159-1162, 2009.

A. Egner, C. Geisler, C. Von-middendorff, H. Bock, D. Wenzel et al., Fluorescence Nanoscopy in Whole Cells by Asynchronous Localization of Photoswitching Emitters, Biophys. J, vol.93, pp.3285-3290, 2007.

P. Ellinger and A. Hirt, Mikroskopische Beobachtungen an lebenden Organen mit Demonstrationen (Intravitalmikroskopie), Arch Exp Pathol Phar, vol.147, p.63, 1929.

D. Elmlund and H. Elmlund, SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles, J. Struct. Biol, vol.180, pp.420-427, 2012.

J. Enderlein, E. Toprak, and P. R. Selvin, Polarization effect on position accuracy of fluorophore localization, Opt. Express, vol.14, pp.8111-8120, 2006.

U. Endesfelder, K. Finan, S. J. Holden, P. R. Cook, A. N. Kapanidis et al.,

, Multiscale Spatial Organization of RNA Polymerase in Escherichia coli, Biophys. J, vol.105, pp.172-181

J. Engelhardt, J. Keller, P. Hoyer, M. Reuss, T. Staudt et al., Molecular Orientation Affects Localization Accuracy in Superresolution Far-Field Fluorescence Microscopy, Nano Lett, vol.11, pp.209-213, 2011.

J. Fölling, M. Bossi, H. Bock, R. Medda, C. A. Wurm et al., Fluorescence nanoscopy by ground-state depletion and singlemolecule return, Nat. Methods, vol.5, pp.943-945, 2008.

D. R. Foltz, L. E. Jansen, A. O. Bailey, J. R. Yates, E. A. Bassett et al., Centromere-Specific Assembly of CENP-A Nucleosomes Is Mediated by HJURP, Cell, vol.137, pp.472-484, 2009.

M. R. Foreman, C. M. Romero, and P. Török, Determination of the three-dimensional orientation of single molecules, Opt. Lett, vol.33, pp.1020-1022, 2008.

R. Förster, K. Wicker, W. Müller, A. Jost, and R. Heintzmann, Motion artefact detection in structured illumination microscopy for live cell imaging, Opt. Express, vol.24, pp.22121-22134, 2016.

T. Fukagawa and W. C. Earnshaw, The Centromere: Chromatin Foundation for the Kinetochore Machinery, Dev. Cell, vol.30, pp.496-508, 2014.

E. Fussner, R. W. Ching, and D. P. Bazett-jones, Living without 30nm chromatin fibers, Trends Biochem. Sci, vol.36, pp.1-6, 2011.

C. Geisler, A. Schönle, C. Middendorff, H. Bock, C. Eggeling et al., Resolution of ? /10 in fluorescence microscopy using fast single molecule photo-switching, Appl. Phys. A, vol.88, pp.223-226, 2007.

C. Geisler, T. Hotz, A. Schönle, S. W. Hell, A. Munk et al., Drift estimation for single marker switching based imaging schemes, Opt. Express, vol.20, pp.7274-7289, 2012.

C. P. Geiss, D. Keramisanou, N. Sekulic, M. P. Scheffer, B. E. Black et al.,

. Cenp-a, Arrays Are More Condensed than Canonical Arrays at Low Ionic Strength, Biophys. J, vol.106, pp.875-882

J. Gelles, B. J. Schnapp, and M. P. Sheetz, Tracking kinesin-driven movements with nanometre-scale precision, Nature, vol.331, pp.450-453, 1988.

M. Georgieva, D. I. Cattoni, J. Fiche, T. Mutin, D. Chamousset et al., Nanometer resolved single-molecule colocalization of nuclear factors by two-color super resolution microscopy imaging, Methods, vol.105, pp.44-55, 2016.

G. Giannone, E. Hosy, F. Levet, A. Constals, K. Schulze et al., Dynamic Superresolution Imaging of Endogenous Proteins on Living Cells at Ultra-High Density, Biophys. J, vol.99, pp.1303-1310, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00661871

M. P. Gordon, T. Ha, and P. R. Selvin, Single-molecule high-resolution imaging with photobleaching, Proc. Natl. Acad. Sci. U. S. A, vol.101, pp.6462-6465, 2004.

F. Göttfert, T. Pleiner, J. Heine, V. Westphal, D. Görlich et al., , 2017.

, Strong signal increase in STED fluorescence microscopy by imaging regions of subdiffraction extent, Proc. Natl. Acad. Sci, vol.114, pp.2125-2130

J. Griffié, M. Shannon, C. L. Bromley, L. Boelen, G. L. Burn et al., A Bayesian cluster analysis method for single-molecule localization microscopy data, Nat. Protoc, vol.11, pp.2499-2514, 2016.

T. Grotjohann, I. Testa, M. Leutenegger, H. Bock, N. T. Urban et al., Diffraction-unlimited all-optical imaging and writing with a photochromic GFP, Nature, vol.478, pp.204-208, 2011.

J. Grove, D. J. Metcalf, A. E. Knight, S. T. Wavre-shapton, T. Sun et al., Flat clathrin lattices: stable features of the plasma membrane, Mol. Biol. Cell, vol.25, pp.3581-3594, 2014.

M. Guerra, G. Cabral, M. Cuacos, M. González-garcía, M. González-sánchez et al., Neocentrics and Holokinetics (Holocentrics): Chromosomes out of the Centromeric Rules, vol.129, pp.82-96, 2010.

M. Guizar-sicairos, S. T. Thurman, and J. R. Fienup, Efficient subpixel image registration algorithms, Opt. Lett, vol.33, pp.156-158, 2008.

N. G. Gurskaya, V. V. Verkhusha, A. S. Shcheglov, D. B. Staroverov, T. V. Chepurnykh et al., Engineering of a monomeric green-to-red photoactivatable fluorescent protein induced by blue light, Nat. Biotechnol, vol.24, pp.461-465, 2006.

M. G. Gustafsson, Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy, J. Microsc, vol.198, pp.82-87, 2000.

M. G. Gustafsson, Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution, Proc. Natl. Acad. Sci. U. S. A, vol.102, pp.13081-13086, 2005.

A. Gustafsson and S. , I5M: 3D widefield light microscopy with better than 100 nm axial resolution, J. Microsc, vol.195, pp.10-16, 1999.

M. G. Gustafsson, D. A. Agard, and J. W. Sedat, Sevenfold improvement of axial resolution in 3D wide-field microscopy using two objective lenses, pp.147-156, 1995.

M. G. Gustafsson, D. A. Agard, and J. W. Sedat, 3D widefield microscopy with two objective lenses: experimental verification of improved axial resolution, pp.62-66, 1996.

M. G. Gustafsson, L. Shao, P. M. Carlton, C. J. Wang, I. N. Golubovskaya et al., Three-Dimensional Resolution Doubling in Wide-Field Fluorescence Microscopy by Structured Illumination, Biophys. J, vol.94, pp.4957-4970, 2008.

C. Hamers-casterman, T. Atarhouch, S. Muyldermans, G. Robinson, C. Hamers et al., Naturally occurring antibodies devoid of light chains, Nature, vol.363, pp.446-448, 1993.

J. Hanne, F. Göttfert, J. Schimer, M. Anders-Össwein, J. Konvalinka et al., , 2016.

, Nanoscopy Reveals Time-Course of Human Immunodeficiency Virus Proteolytic Maturation, ACS Nano, vol.10, pp.8215-8222

P. E. Hänninen, S. W. Hell, J. Salo, E. Soini, and C. Cremer, Two-photon excitation 4Pi confocal microscope: Enhanced axial resolution microscope for biological research, Appl. Phys. Lett, vol.66, pp.1698-1700, 1995.

B. Harke, J. Keller, C. K. Ullal, V. Westphal, A. Schönle et al., Resolution scaling in STED microscopy, Opt. Express, vol.16, pp.4154-4162, 2008.

M. M. Harmsen and H. J. Haard, Properties, production, and applications of camelid single-domain antibody fragments, Appl. Microbiol. Biotechnol, vol.77, pp.13-22, 2007.

L. J. Harris, E. Skaletsky, and A. Mcpherson, Crystallographic structure of an intact IgG1 monoclonal antibody, J. Mol. Biol, vol.275, pp.861-872, 1998.

M. Van-heel, W. Keegstra, W. Schutter, and E. F. Van-bruggen, Arthropod hemocyanin structures studied by image analysis, Structure and Function of Invertebrate Respiratory Proteins, vol.1, pp.69-73, 1982.

M. Van-heel, G. Harauz, E. V. Orlova, R. Schmidt, and M. Schatz, A new generation of the IMAGIC image processing system, J. Struct. Biol, vol.116, pp.17-24, 1996.

M. Heilemann, E. Margeat, R. Kasper, M. Sauer, and P. Tinnefeld, Carbocyanine Dyes as Efficient Reversible Single-Molecule Optical Switch, J. Am. Chem. Soc, vol.127, pp.3801-3806, 2005.

M. Heilemann, S. Van-de-linde, M. Schüttpelz, R. Kasper, B. Seefeldt et al., Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes, Angew. Chem. Int. Ed, vol.47, pp.6172-6176, 2008.

M. Heilemann, S. Van-de-linde, A. Mukherjee, and M. Sauer, Super-Resolution Imaging with Small Organic Fluorophores, Angew. Chem. Int. Ed, vol.48, pp.6903-6908, 2009.

R. Heintzmann, T. M. Jovin, and C. Cremer, Saturated patterned excitation microscopy-a concept for optical resolution improvement, JOSA A, vol.19, pp.1599-1609, 2002.

S. Hell and E. H. Stelzer, Properties of a 4Pi confocal fluorescence microscope, JOSA A, vol.9, pp.2159-2166, 1992.

S. W. Hell and M. Kroug, Ground-state-depletion fluorscence microscopy: A concept for breaking the diffraction resolution limit, Appl. Phys. B, vol.60, pp.495-497, 1995.

S. W. Hell and J. Wichmann, Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy, Opt. Lett, vol.19, pp.780-782, 1994.

S. W. Hell, S. Lindek, C. Cremer, and E. H. Stelzer, Measurement of the 4Pi-confocal point spread function proves 75 nm axial resolution, Appl. Phys. Lett, vol.64, pp.1335-1337, 1994.

S. W. Hell, M. Dyba, J. , and S. , Concepts for nanoscale resolution in fluorescence microscopy, Curr. Opin. Neurobiol, vol.14, pp.599-609, 2004.

S. W. Hell, R. Schmidt, and A. Egner, Diffraction-unlimited three-dimensional optical nanoscopy with opposing lenses, Nat. Photonics, vol.3, pp.381-387, 2009.

R. Henriques, M. Lelek, E. F. Fornasiero, F. Valtorta, C. Zimmer et al., QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ, Nat. Methods, vol.7, pp.339-340, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02081312

S. T. Hess, T. P. Girirajan, and M. D. Mason, Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy, Biophys. J, vol.91, pp.4258-4272, 2006.

L. Hirvonen, O. Mandula, K. Wicker, and R. Heintzmann, Structured illumination microscopy using photoswitchable fluorescent proteins, pp.68610-68610, 2008.

S. J. Holden, S. Uphoff, and A. N. Kapanidis, DAOSTORM: an algorithm for highdensity super-resolution microscopy, Nat. Methods, vol.8, pp.279-280, 2011.

L. Holtzer, T. Meckel, and T. Schmidt, Nanometric three-dimensional tracking of individual quantum dots in cells, Appl. Phys. Lett, vol.90, p.53902, 2007.

A. Honigmann, V. Mueller, H. Ta, A. Schoenle, E. Sezgin et al.,

, Scanning STED-FCS reveals spatiotemporal heterogeneity of lipid interaction in the plasma membrane of living cells, Nat. Commun, vol.5, p.5412

E. Hoogendoorn, K. C. Crosby, D. Leyton-puig, R. M. Breedijk, K. Jalink et al., The fidelity of stochastic single-molecule super-resolution reconstructions critically depends upon robust background estimation, 2014.

A. E. Horn, J. F. Kugel, and J. A. Goodrich, Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity, Nucleic Acids Res, vol.44, pp.7132-7143, 2016.

B. Huang, W. Wang, M. Bates, and X. Zhuang, Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy, Science, vol.319, pp.810-813, 2008.

B. Huang, S. A. Jones, B. Brandenburg, and X. Zhuang, Whole-cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution, Nat. Methods, vol.5, pp.1047-1052, 2008.

F. Huang, S. L. Schwartz, J. M. Byars, and K. A. Lidke, Simultaneous multipleemitter fitting for single molecule super-resolution imaging, Biomed. Opt. Express, vol.2, pp.1377-1393, 2011.

F. Huang, T. M. Hartwich, F. E. Rivera-molina, Y. Lin, W. C. Duim et al., Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms, Nat. Methods, vol.10, pp.653-658, 2013.

F. Huang, G. Sirinakis, E. S. Allgeyer, L. K. Schroeder, W. C. Duim et al., Ultra-High Resolution 3D Imaging of Whole Cells, Cell, vol.166, pp.1028-1040, 2016.

J. Huff, The Airyscan detector from ZEISS: confocal imaging with improved signalto-noise ratio and super-resolution, Nat. Methods, vol.12, 2015.

M. Irie, T. Fukaminato, T. Sasaki, N. Tamai, and T. Kawai, Organic chemistry: A digital fluorescent molecular photoswitch, Nature, vol.420, pp.759-760, 2002.

I. Izeddin, M. El-beheiry, J. Andilla, D. Ciepielewski, X. Darzacq et al., , 2012.

, PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking, Opt. Express, vol.20, p.4957

A. Jab?o?ski, Efficiency of Anti-Stokes Fluorescence in Dyes, Nature, vol.131, pp.839-840, 1933.

L. E. Jansen, B. E. Black, D. R. Foltz, C. , and D. W. , Propagation of centromeric chromatin requires exit from mitosis, J. Cell Biol, vol.176, pp.795-805, 2007.

S. A. Jones, S. Shim, J. He, and X. Zhuang, Fast, three-dimensional superresolution imaging of live cells, Nat. Methods, vol.8, pp.499-505, 2011.

Y. Joti, T. Hikima, Y. Nishino, F. Kamada, S. Hihara et al., Chromosomes without a 30-nm chromatin fiber, Nucleus, vol.3, pp.404-410, 2012.

M. F. Juette, T. J. Gould, M. D. Lessard, M. J. Mlodzianoski, B. S. Nagpure et al., Three-dimensional, 2008.

M. Kozubek and P. Matula, An efficient algorithm for measurement and correction of chromatic aberrations in fluorescence microscopy, J. Microsc, vol.200, pp.206-217, 2000.

H. Kriegel, P. Kröger, J. Sander, and A. Zimek, Density-based clustering, Wiley Interdiscip. Rev. Data Min. Knowl. Discov, vol.1, pp.231-240, 2011.

T. D. Lacoste, X. Michalet, F. Pinaud, D. S. Chemla, A. P. Alivisatos et al., , 2000.

, Ultrahigh-resolution multicolor colocalization of single fluorescent probes, Proc. Natl. Acad. Sci. 97, pp.9461-9466

J. R. Lakowicz, Fluorescence Anisotropy, Principles of Fluorescence Spectroscopy, pp.353-382, 2006.

P. Larghi, D. J. Williamson, J. Carpier, S. Dogniaux, K. Chemin et al., VAMP7 controls T cell activation by regulating the recruitment and phosphorylation of vesicular Lat at TCR-activation sites, Nat. Immunol, vol.14, pp.723-731, 2013.

A. W. Leising, Y. , and J. , Spacing mechanisms within light-induced copepod swarms, Mar. Ecol. Prog. Ser, vol.155, pp.127-135, 1997.

C. Lemaître, A. Grabarz, K. Tsouroula, L. Andronov, A. Furst et al., Nuclear position dictates DNA repair pathway choice, Genes Dev, vol.28, pp.2450-2463, 2014.

M. D. Lesoine, S. Bose, J. W. Petrich, and E. A. Smith, Supercontinuum Stimulated Emission Depletion Fluorescence Lifetime Imaging, J. Phys. Chem. B, vol.116, pp.7821-7826, 2012.

F. Levet, E. Hosy, A. Kechkar, C. Butler, A. Beghin et al.,

, SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data, Nat. Methods, vol.12, pp.1065-1071

M. D. Lew, M. A. Thompson, M. Badieirostami, and W. E. Moerner, In vivo Three-Dimensional Superresolution Fluorescence Tracking using a Double-Helix Point Spread Function, Proc. SPIE--Int, vol.7571, p.75710, 2010.

M. D. Lew, S. F. Lee, J. L. Ptacin, M. K. Lee, R. J. Twieg et al.,

, Three-dimensional superresolution colocalization of intracellular protein superstructures and the cell surface in live Caulobacter crescentus, Proc. Natl. Acad. Sci, vol.108, pp.1102-1110

D. Li, L. Shao, B. Chen, X. Zhang, M. Zhang et al., Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics, Science, vol.349, p.3500, 2015.

H. Y. Liao and J. Frank, Definition and estimation of resolution in single-particle reconstructions, Struct. Lond. Engl, vol.18, pp.768-775, 1993.

. Long-range, Interactions Reveals Folding Principles of the Human Genome, Science, vol.326, pp.289-293

S. Linde, . Van-de, R. Kasper, M. Heilemann, and M. Sauer, Photoswitching microscopy with standard fluorophores, Appl. Phys. B, vol.93, p.725, 2008.

S. Linde, . Van-de, U. Endesfelder, A. Mukherjee, M. Schüttpelz et al., Multicolor photoswitching microscopy for subdiffraction-resolution fluorescence imaging, Photochem. Photobiol. Sci, vol.8, pp.465-469, 2009.

F. B. Lopes, ?. Bálint, S. Valvo, J. H. Felce, E. M. Hessel et al.,

, Membrane nanoclusters of Fc?RI segregate from inhibitory SIRP? upon activation of human macrophages, J Cell Biol jcb, 201608094.

L. Rayleigh, XXXI. Investigations in optics, with special reference to the spectroscope, Philos. Mag. Ser, vol.5, pp.261-274, 1879.

G. V. Los, L. P. Encell, M. G. Mcdougall, D. D. Hartzell, N. Karassina et al., HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis, ACS Chem. Biol, vol.3, pp.373-382, 2008.

K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent, R. et al., Crystal structure of the nucleosome core particle at 2.8 Å resolution, Nature, vol.389, pp.251-260, 1997.

H. Lu-walther, W. Hou, M. Kielhorn, Y. Arai, T. Nagai et al., Nonlinear Structured Illumination Using a Fluorescent Protein Activating at the Readout Wavelength, PLOS ONE, vol.11, 2016.

K. Maeshima, S. Hihara, and H. Takata, New Insight into the Mitotic Chromosome Structure Irregular Folding of Nucleosome Fibers Without 30-nm Chromatin Structure, Cold Spring Harb. Symp. Quant. Biol, vol.75, pp.439-444, 2010.

S. Malkusch, U. Endesfelder, J. Mondry, M. Gelléri, P. J. Verveer et al.,

, Coordinate-based colocalization analysis of single-molecule localization microscopy data, Histochem. Cell Biol, vol.137, pp.1-10

E. M. Manders, J. Stap, G. J. Brakenhoff, R. Van-driel, and J. A. Aten, Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy, J. Cell Sci, vol.103, pp.857-862, 1992.

E. M. Manders, F. J. Verbeek, and J. A. Aten, Measurement of co-localization of objects in dual-colour confocal images, J. Microsc, vol.169, pp.375-382, 1993.

S. Manley, J. M. Gillette, G. H. Patterson, H. Shroff, H. F. Hess et al., High-density mapping of single-molecule trajectories with photoactivated localization microscopy, Nat. Methods, vol.5, pp.155-157, 2008.

J. B. Manneville, S. Etienne-manneville, P. Skehel, T. Carter, D. Ogden et al.,

K. D. Marjon, C. M. Termini, K. L. Karlen, C. Saito-reis, C. E. Soria et al., Tetraspanin CD82 regulates bone marrow homing of acute myeloid leukemia by modulating the molecular organization of N-cadherin, Oncogene, vol.35, pp.4132-4140, 2016.

J. Mcgrew, B. Diehl, F. , and M. , Single base-pair mutations in centromere element III cause aberrant chromosome segregation in Saccharomyces cerevisiae, Mol. Cell. Biol, vol.6, pp.530-538, 1986.

K. L. Mckinley and I. M. Cheeseman, The molecular basis for centromere identity and function, Nat. Rev. Mol. Cell Biol, vol.17, pp.16-29, 2016.

M. D. Miell, C. J. Fuller, A. Guse, H. M. Barysz, A. Downes et al., CENP-A confers a reduction in height on octameric nucleosomes, Nat. Struct. Mol. Biol, vol.20, pp.763-765, 2013.

M. Mikhaylova, B. M. Cloin, K. Finan, R. Berg, . Van-den et al., Resolving bundled microtubules using anti-tubulin nanobodies, Nat. Commun, vol.6, p.8933, 2015.

M. Minsky, Microscopy apparatus. US patent 3013467 A, 1961.

L. A. Mirny, The fractal globule as a model of chromatin architecture in the cell, Chromosome Res, vol.19, pp.37-51, 2011.

M. J. Mlodzianoski, J. M. Schreiner, S. P. Callahan, K. Smolková, A. Dlasková et al., Sample drift correction in 3D fluorescence photoactivation localization microscopy, Opt. Express, vol.19, p.15009, 2011.

G. Moneron and S. W. Hell, Two-photon excitation STED microscopy, Opt. Express, vol.17, pp.14567-14573, 2009.

L. Nahidiazar, A. V. Agronskaia, J. Broertjes, B. Broek, J. Van-den et al., , 2016.

, Optimizing Imaging Conditions for Demanding Multi-Color Super Resolution Localization Microscopy, PLOS ONE, vol.11, 158884.

M. A. Neil, R. Ju?kaitis, W. , and T. , Method of obtaining optical sectioning by using structured light in a conventional microscope, Opt. Lett, vol.22, pp.1905-1907, 1997.

P. R. Nicovich, D. M. Owen, and K. Gaus, Turning single-molecule localization microscopy into a quantitative bioanalytical tool, Nat. Protoc, vol.12, pp.453-460, 2017.

R. P. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald et al., Measuring image resolution in optical nanoscopy, Nat. Methods, vol.10, pp.557-562, 2013.

H. Nishimune, Y. Badawi, S. Mori, and K. Shigemoto, Dual-color STED microscopy reveals a sandwich structure of Bassoon and Piccolo in active zones of adult and aged mice, Sci. Rep, vol.6, p.27935, 2016.

Y. Nishino, M. Eltsov, Y. Joti, K. Ito, H. Takata et al., , 2012.

, EMBO J, vol.31, pp.1644-1653

M. Oheim, D. Loerke, W. Stuhmer, and R. H. Chow, The last few milliseconds in the life of a secretory granule -Docking, dynamics and fusion visualized by total internal reflection fluorescence microscopy (TIRFM), Eur. Biophys. J. Biophys. Lett, vol.27, pp.83-98, 1998.

A. M. Oijen, . Van, J. Köhler, J. Schmidt, M. Müller et al., Far-field fluorescence microscopy beyond the diffraction limit, JOSA A, vol.16, pp.909-915, 1999.

A. Okabe, B. Boots, K. Sugihara, and S. N. Chiu, Spatial Tessellations: Concepts and Applications of Voronoi Diagrams, 2000.

A. Olichon and T. Surrey, Selection of Genetically Encoded Fluorescent Single Domain Antibodies Engineered for Efficient Expression in Escherichia coli, J. Biol. Chem, vol.282, pp.36314-36320, 2007.

A. L. Olins and D. E. Olins, Spheroid Chromatin Units (? Bodies), Science, vol.183, pp.330-332, 1974.

N. Olivier, D. Keller, V. S. Rajan, P. Gönczy, and S. Manley, Simple buffers for 3D STORM microscopy, Biomed. Opt. Express, vol.4, pp.885-899, 2013.

F. Opazo, M. Levy, M. Byrom, C. Schäfer, C. Geisler et al., Aptamers as potential tools for super-resolution microscopy, Nat. Methods, vol.9, pp.938-939, 2012.

I. Orlov, A. G. Myasnikov, L. Andronov, S. K. Natchiar, H. Khatter et al., The integrative role of cryo electron microscopy in molecular and cellular structural biology, Biol. Cell, vol.109, pp.81-93, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-02409721

P. Oudet, M. Gross-bellard, C. , and P. , Electron microscopic and biochemical evidence that chromatin structure is a repeating unit, Cell, vol.4, pp.281-300, 1975.

M. Ovesný, P. K?í?ek, J. Borkovec, Z. ?vindrych, and G. M. Hagen, ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging, Bioinformatics, vol.30, pp.2389-2390, 2014.

D. M. Owen, C. Rentero, J. Rossy, A. Magenau, D. Williamson et al., PALM imaging and cluster analysis of protein heterogeneity at the cell surface, J. Biophotonics, vol.3, pp.446-454, 2010.

P. Oza, S. L. Jaspersen, A. Miele, J. Dekker, and C. L. Peterson, Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery, Genes Dev, vol.23, pp.912-927, 2009.

A. Padeganeh, J. Ryan, J. Boisvert, A. Ladouceur, J. F. Dorn et al.,

, Octameric CENP-A Nucleosomes Are Present at Human Centromeres throughout the Cell Cycle, Curr. Biol, vol.23, pp.764-769

S. V. Pageon, T. Tabarin, Y. Yamamoto, Y. Ma, P. R. Nicovich et al., Functional role of T-cell receptor nanoclusters in signal initiation and antigen discrimination, Proc. Natl. Acad. Sci, vol.113, pp.5454-5463, 2016.

D. K. Palmer, K. O'day, H. L. Trong, H. Charbonneau, and R. L. Margolis, Purification of the centromere-specific protein CENP-A and demonstration that it is a distinctive histone, Proc. Natl. Acad. Sci. U. S. A, vol.88, pp.3734-3738, 1991.

T. Panchenko, T. C. Sorensen, C. L. Woodcock, Z. Kan, S. Wood et al., Replacement of histone H3 with CENP-A directs global nucleosome array condensation and loosening of nucleosome superhelical termini, Proc. Natl. Acad. Sci, vol.108, pp.16588-16593, 2011.

G. H. Patterson and J. Lippincott-schwartz, A Photoactivatable GFP for Selective Photolabeling of Proteins and Cells, Science, vol.297, pp.1873-1877, 2002.

S. R. Pavani and R. Piestun, High-efficiency rotating point spread functions, Opt. Express, vol.16, pp.3484-3489, 2008.

S. R. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu et al., Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function, Proc. Natl. Acad. Sci, vol.106, pp.2995-2999, 2009.

K. Pearson, Mathematical Contributions to the Theory of Evolution, III. Regression, Heredity, and Panmixia. Philos. Trans. R. Soc. Lond. Math. Phys. Eng. Sci, vol.187, pp.253-318, 1896.

T. Pengo, S. J. Holden, and S. Manley, PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy, Bioinforma. Oxf. Engl, vol.31, pp.797-798, 2015.

E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt et al., UCSF Chimera--a visualization system for exploratory research and analysis, J. Comput. Chem, vol.25, pp.1605-1612, 2004.

T. Pleiner, M. Bates, S. Trakhanov, C. Lee, J. E. Schliep et al., Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation, 2015.

T. Quan, H. Zhu, X. Liu, Y. Liu, J. Ding et al., High-density localization of active molecules using Structured Sparse Model and Bayesian Information Criterion, Opt. Express, vol.19, pp.16963-16974, 2011.

F. Rahbarizadeh, M. J. Rasaee, M. Forouzandeh-moghadam, A. , and A. , , 2005.

, High expression and purification of the recombinant camelid anti-MUC1 single domain antibodies in Escherichia coli, Protein Expr. Purif, vol.44, pp.32-38

E. H. Rego, L. Shao, J. J. Macklin, L. Winoto, G. A. Johansson et al., Nonlinear structured-illumination microscopy with a photoswitchable protein reveals cellular structures at 50-nm resolution, Proc. Natl. Acad. Sci, vol.109, pp.135-143, 2012.

J. Reindl, S. Girst, D. W. Walsh, C. Greubel, B. Schwarz et al., Chromatin organization revealed by nanostructure of irradiation induced ?H2AX, 53BP1 and Rad51 foci, Sci. Rep, vol.7, p.40616, 2017.

S. A. Ribeiro, P. Vagnarelli, Y. Dong, T. Hori, B. F. Mcewen et al., A super-resolution map of the vertebrate kinetochore, Proc. Natl. Acad. Sci, vol.107, pp.10484-10489, 2010.

T. Ribeiro, A. Marques, P. Novák, V. Schubert, A. L. Vanzela et al., Centromeric and non-centromeric satellite DNA organisation differs in holocentric Rhynchospora species, Chromosoma, vol.126, pp.325-335, 2017.

M. A. Ricci, C. Manzo, M. F. García-parajo, M. Lakadamyali, and M. P. Cosma, , 2015.

, Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo, Cell, vol.160, pp.1145-1158

J. Ries, C. Kaplan, E. Platonova, H. Eghlidi, and H. Ewers, A simple, versatile method for GFP-based super-resolution microscopy via nanobodies, Nat. Methods, vol.9, pp.582-584, 2012.

B. D. Ripley, The Second-Order Analysis of Stationary Point Processes, J. Appl. Probab, vol.13, pp.255-266, 1976.

B. D. Ripley, Tests of `Randomness' for Spatial Point Patterns, J. R. Stat. Soc. Ser. B Methodol, vol.41, pp.368-374, 1979.

E. Rittweger, K. Y. Han, S. E. Irvine, C. Eggeling, and S. W. Hell, STED microscopy reveals crystal colour centres with nanometric resolution, Nat. Photonics, vol.3, pp.144-147, 2009.

A. S. Rose and P. W. Hildebrand, NGL Viewer: a web application for molecular visualization, Nucleic Acids Res, vol.43, pp.576-579, 2015.

J. Rossy, D. M. Owen, D. J. Williamson, Z. Yang, and K. Gaus, Conformational states of the kinase Lck regulate clustering in early T cell signaling, Nat. Immunol, vol.14, pp.82-89, 2013.

J. Rossy, E. Cohen, K. Gaus, and D. M. Owen, Method for co-cluster analysis in multichannel single-molecule localisation data, Histochem. Cell Biol, vol.141, pp.605-612, 2014.

H. Ruan, J. Yu, J. Yuan, N. Li, and X. Fang, Nanoscale Distribution of Transforming Growth Factor Receptor on Post-Golgi Vesicle Revealed by Super-resolution Microscopy, Chem. -Asian J, vol.11, pp.3359-3364, 2016.

P. Rubin-delanchy, G. L. Burn, J. Griffié, D. J. Williamson, N. A. Heard et al., Bayesian cluster identification in single-molecule localization microscopy data, Nat. Methods, vol.12, pp.1072-1076, 2015.

M. J. Rust, M. Bates, and X. Zhuang, Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM), Nat. Methods, vol.3, pp.793-796, 2006.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min et al., , 2015.

, Quantitative evaluation of software packages for single-molecule localization microscopy, Nat. Methods, vol.12, pp.717-724

I. Samejima, C. Spanos, F. Alves, L. De, T. Hori et al., Whole-proteome genetic analysis of dependencies in assembly of a vertebrate kinetochore, J. Cell Biol, vol.211, pp.1141-1156, 2015.

S. Santaguida and A. Musacchio, The life and miracles of kinetochores, EMBO J, vol.28, pp.2511-2531, 2009.

W. O. Saxton and W. Baumeister, The correlation averaging of a regularly arranged bacterial cell envelope protein, J. Microsc, vol.127, pp.127-138, 1982.

L. H. Schaefer, D. Schuster, and J. Schaffer, Structured illumination microscopy: artefact analysis and reduction utilizing a parameter optimization approach, J. Microsc, vol.216, pp.165-174, 2004.

L. Schermelleh, P. M. Carlton, S. Haase, L. Shao, L. Winoto et al., Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy, Science, vol.320, pp.1332-1336, 2008.

L. Schermelleh, R. Heintzmann, and H. Leonhardt, A guide to super-resolution fluorescence microscopy, J. Cell Biol, vol.190, pp.165-175, 2010.

T. Schmidt, G. J. Schütz, W. Baumgartner, H. J. Gruber, and H. Schindler, Imaging of single molecule diffusion, Proc. Natl. Acad. Sci, vol.93, pp.2926-2929, 1996.

J. J. Schmied, M. Raab, C. Forthmann, E. Pibiri, B. Wünsch et al., DNA origami-based standards for quantitative fluorescence microscopy, Nat. Protoc, vol.9, pp.1367-1391, 2014.

P. Sengupta, T. Jovanovic-talisman, D. Skoko, M. Renz, S. L. Veatch et al., Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis, Nat. Methods, vol.8, pp.969-975, 2011.

P. Sengupta, T. Jovanovic-talisman, and J. Lippincott-schwartz, Quantifying spatial organization in point-localization superresolution images using pair correlation analysis, Nat. Protoc, vol.8, pp.345-354, 2013.

N. C. Shaner, R. E. Campbell, P. A. Steinbach, B. N. Giepmans, A. E. Palmer et al., Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein, Nat. Biotechnol, vol.22, pp.1567-1572, 2004.

C. J. Sheppard and A. Choudhury, Image Formation in the Scanning Microscope, Opt. Acta Int. J. Opt, vol.24, pp.1051-1073, 1977.

O. Shimomura, F. H. Johnson, and Y. Saiga, Extraction, Purification and Properties of Aequorin, a Bioluminescent Protein from the Luminous Hydromedusan, Aequorea. J. Cell. Comp. Physiol, vol.59, pp.223-239, 1962.

I. Shiraishi, T. Takamatsu, T. Minamikawa, and S. Fujita, , 1992.

, Anat. Embryol. (Berl.), vol.185, pp.401-408

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics, Nat. Methods, vol.5, pp.417-423, 2008.

G. Shtengel, J. A. Galbraith, C. G. Galbraith, J. Lippincott-schwartz, J. M. Gillette et al., , 2009.

, Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure, Proc. Natl. Acad. Sci, vol.106, pp.3125-3130

M. Shuaib, K. Ouararhni, S. Dimitrov, and A. Hamiche, HJURP binds CENP-A via a highly conserved N-terminal domain and mediates its deposition at centromeres, Proc. Natl. Acad. Sci, vol.107, pp.1349-1354, 2010.

B. L. Sinnen, A. B. Bowen, J. S. Forte, B. G. Hiester, K. C. Crosby et al., Optogenetic Control of Synaptic Composition and Function, Neuron, vol.93, pp.646-660, 2017.

A. Small and S. Stahlheber, Fluorophore localization algorithms for super-resolution microscopy, Nat. Methods, vol.11, pp.267-279, 2014.

C. S. Smith, N. Joseph, B. Rieger, and K. A. Lidke, Fast, single-molecule localization that achieves theoretically minimum uncertainty, Nat. Methods, vol.7, pp.373-375, 2010.

S. Spinelli, L. Frenken, D. Bourgeois, L. Ron, . De et al., The crystal structure of a llama heavy chain variable domain, Nat. Struct. Mol. Biol, vol.3, pp.752-757, 1996.

S. Stallinga and B. Rieger, Accuracy of the Gaussian Point Spread Function model in 2D localization microscopy, Opt. Express, vol.18, pp.24461-24476, 2010.

S. Stallinga and B. Rieger, Position and orientation estimation of fixed dipole emitters using an effective Hermite point spread function model, Opt. Express, vol.20, pp.5896-5921, 2012.

A. C. Stiel, S. Trowitzsch, G. Weber, M. Andresen, C. Eggeling et al., 1.8 Å bright-state structure of the reversibly switchable fluorescent protein Dronpa guides the generation of fast switching variants, Biochem. J, vol.402, pp.35-42, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00478663

A. C. Stiel, M. Andresen, H. Bock, M. Hilbert, J. Schilde et al., Generation of Monomeric Reversibly Switchable Red Fluorescent Proteins for Far-Field Fluorescence Nanoscopy, Biophys. J, vol.95, pp.2989-2997, 2008.

G. G. Stokes, Ueber die Veränderung der Brechbarkeit des Lichts, Ann. Phys, vol.163, pp.480-490, 1852.

D. Stoyan and H. Stoyan, Fractals, random shapes, and point fields: methods of geometrical statistics, 1994.

Y. Sun, J. D. Mckenna, J. M. Murray, E. M. Ostap, and Y. E. Goldman, Parallax: high accuracy three-dimensional single molecule tracking using split images, Nano Lett, vol.9, pp.2676-2682, 2009.

E. J. Sundberg and R. A. Mariuzza, Molecular recognition in antibody-antigen complexes, Adv. Protein Chem, vol.61, pp.119-160, 2002.

A. Szczurek, L. Klewes, J. Xing, A. Gourram, U. Birk et al., Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations, Nucleic Acids Res, vol.45, p.56, 2017.

A. Szymborska, A. Marco, . De, N. Daigle, V. C. Cordes et al., Nuclear Pore Scaffold Structure Analyzed by Super-Resolution Microscopy and Particle Averaging, Science, vol.341, pp.655-658, 2013.

I. Testa, C. A. Wurm, R. Medda, E. Rothermel, C. Von-middendorf et al., Multicolor Fluorescence Nanoscopy in Fixed and Living Cells by Exciting Conventional Fluorophores with a Single Wavelength, Biophys. J, vol.99, pp.2686-2694, 2010.

R. E. Thompson, D. R. Larson, and W. W. Webb, Precise nanometer localization analysis for individual fluorescent probes, Biophys. J, vol.82, pp.2775-2783, 2002.

C. Tilke, Statistics for spatial data, Comput. Stat. Data Anal, vol.920, pp.547-544, 1991.

D. K. Tiwari, Y. Arai, M. Yamanaka, T. Matsuda, M. Agetsuma et al., A fast-and positively photoswitchable fluorescent protein for ultralowlaser-power RESOLFT nanoscopy, Nat. Methods, vol.12, pp.515-518, 2015.

J. Tønnesen, F. Nadrigny, K. I. Willig, R. Wedlich-söldner, and U. V. Nägerl, Two-Color STED Microscopy of Living Synapses Using A Single Laser-Beam Pair, Biophys. J, vol.101, pp.2545-2552, 2011.

R. D. Vale, T. Funatsu, D. W. Pierce, L. Romberg, Y. Harada et al., , 1996.

, Direct observation of single kinesin molecules moving along microtubules, Nature, vol.380, pp.451-453

M. Van-heel, Angular reconstitution: A posteriori assignment of projection directions for 3D reconstruction, Ultramicroscopy, vol.21, pp.111-123, 1987.

S. L. Veatch, B. B. Machta, S. A. Shelby, E. N. Chiang, D. A. Holowka et al., Correlation Functions Quantify Super-Resolution Images and Estimate Apparent Clustering Due to Over-Counting, PLOS ONE, vol.7, p.31457, 2012.

G. Vicidomini, G. Moneron, K. Y. Han, V. Westphal, H. Ta et al., Sharper low-power STED nanoscopy by time gating, Nat. Methods, vol.8, pp.571-573, 2011.

G. Vicidomini, A. Schönle, H. Ta, K. Y. Han, G. Moneron et al.,

, STED nanoscopy with time-gated detection: theoretical and experimental aspects, PloS One, vol.8, p.54421

G. Voronoi, Nouvelles applications des paramètres continus à la théorie des formes quadratiques, J. Für Reine Angew. Math, pp.97-102, 1908.

A. R. Wade and F. W. Fitzke, A fast, robust pattern recognition system for low light level image registration and its application to retinal imaging, Opt. Express, vol.3, pp.190-197, 1998.

Y. Wang, J. Gao, X. Guo, T. Tong, X. Shi et al., Regulation of EGFR nanocluster formation by ionic protein-lipid interaction, Cell Res, vol.24, pp.959-976, 2014.

Y. Wang, S. Maharana, M. D. Wang, and G. V. Shivashankar, , 2014.

E. S. Ward, D. Güssow, A. D. Griffiths, P. T. Jones, and G. Winter, Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli, Nature, vol.341, pp.544-546, 1989.

E. Wegel, A. Göhler, B. C. Lagerholm, A. Wainman, S. Uphoff et al., Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison, Sci. Rep, vol.6, p.27290, 2016.

V. Westphal and S. W. Hell, Nanoscale Resolution in the Focal Plane of an Optical Microscope, Phys. Rev. Lett, vol.94, p.143903, 2005.

J. G. White, W. B. Amos, and M. Fordham, An evaluation of confocal versus conventional imaging of biological structures by fluorescence light microscopy, J. Cell Biol, vol.105, pp.41-48, 1987.

D. J. Williamson, D. M. Owen, J. Rossy, A. Magenau, M. Wehrmann et al., Pre-existing clusters of the adaptor Lat do not participate in early T cell signaling events, Nat. Immunol, vol.12, pp.655-662, 2011.

T. Wilson, Resolution and optical sectioning in the confocal microscope, J. Microsc, vol.244, pp.113-121, 2011.

C. L. Woodcock, J. P. Safer, and J. E. Stanchfield, Structural repeating units in chromatin, Exp. Cell Res, vol.97, pp.101-110, 1976.

K. Xu, H. P. Babcock, and X. Zhuang, Dual-objective STORM reveals threedimensional filament organization in the actin cytoskeleton, Nat. Methods, vol.9, pp.185-188, 2012.

F. Yang, L. G. Moss, and G. N. Phillips, The molecular structure of green fluorescent protein, Nat. Biotechnol, vol.14, pp.1246-1251, 1996.

A. Yildiz, J. N. Forkey, S. A. Mckinney, T. Ha, Y. E. Goldman et al., , 2003.

V. Myosin and . Hand-over-hand, Single Fluorophore Imaging with 1.5-nm Localization, vol.300, pp.2061-2065

W. Zhang, S. U. Colmenares, and G. H. Karpen, Assembly of Drosophila Centromeric Nucleosomes Requires CID Dimerization, Mol. Cell, vol.45, pp.263-269, 2012.

X. Zhang, M. Zhang, D. Li, W. He, J. Peng et al., Highly photostable, reversibly photoswitchable fluorescent protein with high contrast ratio for livecell superresolution microscopy, Proc. Natl. Acad. Sci, vol.113, pp.10364-10369, 2016.

J. Zhao, S. Bruck, S. Cemerski, L. Zhang, B. Butler et al., CD2AP Links Cortactin and Capping Protein at the Cell Periphery To Facilitate Formation of Lamellipodia, Mol. Cell. Biol, vol.33, pp.38-47, 2013.

B. Zhou, J. Jiang, H. Feng, R. Ghirlando, T. S. Xiao et al., Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks, Appendix References Aymard F, vol.59, pp.366-374, 2014.

A. Beucher, J. Birraux, L. Tchouandong, O. Barton, A. Shibata et al., ATM and Artemis promote homologous recombination of radiation-induced DNA double-strand breaks in G2, Embo J, vol.28, pp.3413-3427, 2009.

W. A. Bickmore, The spatial organization of the human genome, Annu Rev Genomics Hum Genet, vol.14, pp.67-84, 2013.

S. Britton, J. Coates, and S. P. Jackson, A new method for highresolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair, J Cell Biol, vol.202, pp.579-595, 2013.

S. F. Bunting, E. Call-en, N. Wong, H. Chen, F. Polato et al., 53BP1 inhibits homologous recombination in Brca1-deficient cells by blocking resection of DNA breaks, Nuclear architecture regulates DNA repair GENES & DEVELOPMENT 2461, vol.141, pp.243-254, 2010.

J. R. Chapman, T. Martin, R. G. , B. Simon, and J. , Playing the end game: DNA double-strand break repair pathway choice, Mol Cell, vol.47, pp.497-510, 2012.

L. Chen, C. J. Nievera, A. Lee, and X. Wu, Cell cycle-dependent complex formation of BRCA1ÁCtIPÁMRN is important for DNA double-strand break repair, J Biol Chem, vol.283, pp.7713-7720, 2008.

I. Chiolo, A. Minoda, C. Serafin, U. Polyzos, A. et al., Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair, Cell, vol.144, pp.732-744, 2011.

J. R. Chubb, S. Boyle, P. Perry, and W. A. Bickmore, Chromatin motion is constrained by association with nuclear compartments in human cells, Curr Biol, vol.12, pp.439-445, 2002.

S. K. Deng, B. Gibb, M. J. De-almeida, E. C. Greene, and L. S. Symington, RPA antagonizes microhomology-mediated repair of DNA double-strand breaks, Nat Struct Mol Biol, vol.21, pp.405-412, 2014.

V. Dion and S. M. Gasser, Chromatin movement in the maintenance of genome stability, Cell, vol.152, pp.1355-1364, 2013.

V. Dion, V. Kalck, C. Horigome, B. D. Towbin, and S. M. Gasser, Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery, Nat Cell Biol, vol.14, pp.502-509, 2012.

L. E. Finlan, D. Sproul, I. Thomson, S. Boyle, E. Kerr et al., Recruitment to the nuclear periphery can alter expression of genes in human cells, PLoS Genet, vol.4, p.1000039, 2008.

J. Folling, M. Bossi, H. Bock, R. Medda, C. A. Wurm et al., Fluorescence nanoscopy by ground-state depletion and single-molecule return, Nat Methods, vol.5, pp.943-945, 2008.

P. Frit, N. Barboule, Y. Yuan, D. Gomez, and P. Calsou, Alternative end-joining pathway(s): Bricolage at DNA breaks, DNA Repair, vol.17, pp.81-97, 2014.

V. Geuting, C. Reul, and M. L?, ATM release at resected double-strand breaks provides heterochromatin reconstitution to facilitate homologous recombination, PLoS Genet, vol.9, p.1003667, 2013.

A. A. Goodarzi and P. A. Jeggo, The heterochromatic barrier to DNA double strand break repair: how to get the entry visa, Int J Mol Sci, vol.13, pp.11844-11860, 2012.

C. Horigome, Y. Oma, T. Konishi, R. Schmid, I. Marcomini et al., SWR1 and INO80 chromatin remodelers contribute to DNA double-strand break perinuclear anchorage site choice, Mol Cell, vol.55, pp.626-639, 2014.

S. P. Jackson and J. Bartek, The DNA-damage response in human biology and disease, Nature, vol.461, pp.1071-1078, 2009.

B. Jakob, J. Splinter, S. Conrad, K. O. Voss, D. Zink et al., DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin, Nucleic Acids Res, vol.39, pp.6489-6499, 2011.

D. K. Jha and B. D. Strahl, An RNA polymerase II-coupled function for histone H3K36 methylation in checkpoint activation and DSB repair, Nat Commun, 2014.

A. Kakarougkas, A. Ismail, K. Klement, A. A. Goodarzi, S. Conrad et al., Opposing roles for 53BP1 during homologous recombination, Nucleic Acids Res, vol.41, pp.9719-9731, 2013.

E. M. Kass and M. Jasin, Collaboration and competition between DNA double-strand break repair pathways, FEBS Lett, vol.584, pp.3703-3708, 2010.

B. Khadaroo, M. T. Teixeira, P. Luciano, N. Eckert-boulet, S. M. Germann et al.,

, The DNA damage response at eroded telomeres and tethering to the nuclear pore complex, Nat Cell Biol, vol.11, pp.980-987

J. Kind, L. Pagie, H. Ortabozkoyun, S. Boyle, S. S. De-vries et al., Single-cell dynamics of genome-nuclear lamina interactions, Cell, vol.153, pp.178-192, 2013.

C. Lemaître and E. Soutoglou, Double strand break (DSB) repair in heterochromatin and heterochromatin proteins in DSB repair, DNA Repair, vol.19, pp.163-168, 2014.

C. Lemaître, B. Fischer, A. Kalousi, A. S. Hoffbeck, J. Guirouilh-barbat et al., The nucleoporin 153, a novel factor in double-strand break repair and DNA damage response, Oncogene, vol.31, pp.4803-4809, 2012.

M. R. Lieber, The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway, Annu Rev Biochem, vol.79, pp.181-211, 2010.

M. Lisby, U. H. Mortensen, and R. Rothstein, Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre, Nat Cell Biol, vol.5, pp.572-577, 2003.

R. Mahen, H. Hattori, M. Lee, P. Sharma, A. D. Jeyasekharan et al., A-type lamins maintain the positional stability of DNA damage repair foci in mammalian nuclei, PLoS ONE, vol.8, p.61893, 2013.

W. Meuleman, D. Peric-hupkes, J. Kind, J. B. Beaudry, L. Pagie et al., Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence, Genome Res, vol.23, pp.270-280, 2013.

J. Mine-hattab and R. Rothstein, Increased chromosome mobility facilitates homology search during recombination, Nat Cell Biol, vol.14, pp.510-517, 2012.

T. Misteli and E. Soutoglou, The emerging role of nuclear architecture in DNA repair and genome maintenance, Nat Rev Mol Cell Biol, vol.10, pp.243-254, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00384503

S. Nagai, K. Dubrana, M. Tsai-pflugfelder, M. B. Davidson, T. M. Roberts et al., Functional targeting of DNA damage to a nuclear poreassociated SUMO-dependent ubiquitin ligase, Science, vol.322, pp.597-602, 2008.

F. R. Neumann, V. Dion, L. R. Gehlen, M. Tsai-pflugfelder, R. Schmid et al., Targeted INO80 enhances subnuclear chromatin movement and ectopic homologous recombination, Genes Dev, vol.26, pp.369-383, 2012.

P. Oza, S. L. Jaspersen, A. Miele, J. Dekker, and C. L. Peterson, Mechanisms that regulate localization of a DNA doublestrand break to the nuclear periphery, Genes Dev, vol.23, pp.912-927, 2009.

J. Padeken and P. Heun, Nucleolus and nuclear periphery: velcro for heterochromatin, Curr Opin Cell Biol, vol.28, pp.54-60, 2014.

C. C. Pai, R. S. Deegan, L. Subramanian, C. Gal, S. Sarkar et al., A histone H3K36 chromatin switch coordinates DNA doublestrand break repair pathway choice, Nat Commun, 2014.

S. Panier and S. J. Boulton, Double-strand break repair: 53BP1 comes into focus, Nat Rev Mol Cell Biol, vol.15, pp.7-18, 2014.

T. Pankotai, C. Bonhomme, D. Chen, and E. Soutoglou, DNAPKcs-dependent arrest of RNA polymerase II transcription in the presence of DNA breaks, Nat Struct Mol Biol, vol.19, pp.276-282, 2012.

L. A. Parada and T. Misteli, Chromosome positioning in the interphase nucleus, Trends Cell Biol, vol.12, pp.425-432, 2002.

S. X. Pfister, S. Ahrabi, L. P. Zalmas, S. Sarkar, F. Aymard et al.,

. Lemaître,

, GENES & DEVELOPMENT Cold Spring Harbor Laboratory Press on November 10, vol.7, pp.2006-2018, 2017.

C. Ptak, J. D. Aitchison, and R. W. Wozniak, The multifunctional nuclear pore complex: a platform for controlling gene expression, Curr Opin Cell Biol, vol.28, pp.46-53, 2014.

K. L. Reddy, J. M. Zullo, E. Bertolino, and H. Singh, Transcriptional repression mediated by repositioning of genes to the nuclear lamina, Nature, vol.452, pp.243-247, 2008.

E. P. Rogakou, D. R. Pilch, A. H. Orr, V. S. Ivanova, and W. M. Bonner, DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139, J Biol Chem, vol.273, pp.5858-5868, 1998.

V. Roukos and T. Misteli, The biogenesis of chromosome translocations, Nat Cell Biol, vol.16, pp.293-300, 2014.

V. Roukos, T. C. Voss, C. K. Schmidt, S. Lee, D. Wangsa et al., Spatial dynamics of chromosome translocations in living cells, Science, vol.341, pp.660-664, 2013.

S. Filippo, J. Sung, P. Klein, and H. , Mechanism of eukaryotic homologous recombination, Annu Rev Biochem, vol.77, pp.229-257, 2008.

H. Schober, H. Ferreira, V. Kalck, L. R. Gehlen, and S. M. Gasser, Yeast telomerase and the SUN domain protein Mps3 anchor telomeres and repress subtelomeric recombination, Genes Dev, vol.23, pp.928-938, 2009.

E. Soutoglou and T. Misteli, Activation of the cellular DNA damage response in the absence of DNA lesions, Science, vol.320, pp.1507-1510, 2008.

E. Soutoglou, J. F. Dorn, K. Sengupta, M. Jasin, A. Nussenzweig et al., Positional stability of single double-strand breaks in mammalian cells, Nat Cell Biol, vol.9, pp.675-682, 2007.

A. Taddei, G. Van-houwe, F. Hediger, V. Kalck, F. Cubizolles et al., Nuclear pore association confers optimal expression levels for an inducible yeast gene, Nature, vol.441, pp.774-778, 2006.

P. Therizols, C. Fairhead, G. G. Cabal, A. Genovesio, J. C. Olivo-marin et al., Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region, J Cell Biol, vol.172, pp.189-199, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02425531

Y. Zhang and M. Jasin, An essential role for CtIP in chromosomal translocation formation through an alternative endjoining pathway, Nuclear architecture regulates DNA repair GENES & DEVELOPMENT 2463, vol.18, pp.80-84, 2011.

I. Orlov, *. , A. G. Myasnikov*-?-?-§, L. Andronov, *. et al.,

*. Centre-for-integrative-biology, ;. Inserm)-u964, F. Illkirch, and . Strasbourg, France After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo-EM) is now heading off at unprecedented speed towards high-resolution analysis of biological objects of various sizes. This 'revolution in resolution' is happening largely thanks to new developments of new-generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo-EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo-EM in synergy with other methods such as X-ray crystallography, fluorescence imaging or focussed-ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi-scale and multi-resolution approaches allow integrating molecular and

, Key words: cryo electron microscopy, cryo electron tomography, Crystallography, Super-resolution microscopy, Structural biology, To whom correspondence should be addressed (email: klaholz@igbmc.fr) 2 Present address: European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, vol.1, p.69117

, CMOS, complementary metal oxide semiconductor

, DDD, direct detection device

, DQE, detective quantum efficiency; EcR, ecdysone receptor; FIB, focussed-ion beam; FRISBI, French Infrastructure for Integrated Structural Biology; Instruct, Integrated Structural Biology Infrastructure for Europe; kDa

, MSA, multi-variate statistical analysis; mRNA, messenger RNA; rRNA, ribosomal RNA; SEM, scanning electron microscopy

, SMLM, single-molecule localisation microscopy; tRNA, transfer RNA; 2D, two dimensional

. 3d, P. D. Adams, D. Baker, A. T. Brunger, R. Das et al., Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems, Annu. Rev. Biophys, vol.42, pp.265-287, 2013.

Z. A. Afonina, A. G. Myasnikov, V. A. Shirokov, B. P. Klaholz, and A. S. Spirin, Conformation transitions of eukaryotic polyribosomes during multi-round translation, Nucleic Acids Res, vol.43, pp.618-628, 2015.

Z. A. Afonina, A. G. Myasnikov, V. A. Shirokov, B. P. Klaholz, and A. S. Spirin, Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study, Nucleic Acids Res, vol.42, pp.9461-9469, 2014.

P. V. Afonine, R. W. Grosse-kunstleve, N. Echols, J. J. Headd, N. W. Moriarty et al., Toward automated crystallographic structure refinement with phenix.refine, Acta Cryst, vol.68, pp.352-367, 2012.

M. Allegretti, D. J. Mills, G. Mcmullan, W. Kühlbrandt, and J. Vonck, Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector, Elife, vol.3, p.1963, 2014.

L. Andronov, Y. Lutz, J. Vonesch, and B. P. Klaholz, SharpViSu: integrated analysis and segmentation of super-resolution microscopy data, Bioinformatics, vol.32, pp.2239-2241, 2016.

L. Andronov, I. Orlov, Y. Lutz, J. Vonesch, and B. P. Klaholz, ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy, Sci. Rep, vol.6, p.24084, 2016.

J. Arnold, J. Mahamid, V. Lucic, A. De-marco, J. J. Fernandez et al., Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy, Biophys. J, vol.110, pp.860-869, 2016.

S. Asano, B. D. Engel, and W. Baumeister, Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology, vol.428, pp.332-343, 2016.

X. C. Bai, I. S. Fernandez, G. Mcmullan, and S. H. Scheres, Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles, vol.2, p.461, 2013.

N. J. Baird, S. J. Ludtke, H. Khant, W. Chiu, T. Pan et al., Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy, J. Am. Chem. Soc, vol.132, pp.16352-163523, 2010.

S. Banerjee, A. Bartesaghi, A. Merk, P. Rao, S. L. Bulfer et al., ) 2.3Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition, Science, vol.351, pp.871-875, 2016.

B. A. Barad, N. Echols, R. Y. Wang, Y. Cheng, F. Dimaio et al., EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy, Nat. Methods, vol.12, pp.943-946, 2015.

M. Beck, F. Förster, M. Ecke, J. M. Plitzko, F. Melchior et al., Nuclear pore complex structure and dynamics revealed by cryoelectron tomography, Science, vol.306, pp.1387-1390, 2004.

B. Beinsteiner, J. Michalon, and B. P. Klaholz, IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes, Bioinformatics, vol.31, pp.3339-3344, 2015.

A. Ben-shem, L. Jenner, G. Yusupova, and M. Yusupov, Crystal structure of the eukaryotic ribosome, Science, vol.330, pp.1203-1209, 2010.

F. Brandt, L. A. Carlson, F. U. Hartl, W. Baumeister, and K. Grünewald, The three-dimensional organization of polyribosomes in intact human cells, Mol. Cell, vol.39, pp.560-569, 2010.

J. A. Briggs, Structural biology in situ -the potential of subtomogram averaging, Curr. Opin. Struct. Biol, vol.23, pp.261-267, 2013.

A. F. Brilot, J. Z. Chen, A. Cheng, J. Pan, S. C. Harrison et al., Beam-induced motion of vitrified specimen on holey carbon film, J. Struct. Biol, vol.177, pp.630-637, 2012.

C. Broennimann, E. F. Eikenberry, B. Henrich, R. Horisberger, G. Huelsen et al., The PILATUS 1M detector, J. Synchrotron Radiat, vol.13, pp.120-130, 2006.

A. Brown, F. Long, R. A. Nicholls, J. Toots, P. Emsley et al., Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions, Acta Crystallogr. D Biol. Crystallogr, vol.71, pp.136-153, 2015.

M. G. Campbell, A. Cheng, A. F. Brilot, A. Moeller, D. Lyumkis et al., Movies of ice-embedded particles enhance resolution in electron cryo-microscopy, Structure, vol.20, pp.1823-1828, 2012.

J. M. Carazo, C. O. Sorzano, J. Otón, R. Marabini, and J. Vargas, Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data, Arch. Biochem. Biophys, vol.581, pp.39-48, 2015.

M. Carroni and H. R. Saibil, Cryo electron microscopy to determine the structure of macromolecular complexes, Methods, vol.95, pp.78-85, 2016.

A. Casanas, R. Warshamanage, A. D. Finke, E. Panepucci, V. Olieric et al., EIGER detector: application in macromolecular crystallography, Acta Crystallogr. D Struct. Biol, vol.72, pp.1036-1048, 2016.

D. Castaño-díez, M. Kudryashev, and H. Stahlberg, Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms, J. Struct. Biol, vol.16, pp.30111-30113, 2016.

Y. W. Chang, L. A. Rettberg, A. Treuner-lange, J. Iwasa, L. Søgaard-andersen et al., Architecture of the type IVa pilus machine, Science, vol.351, p.2001, 2016.

B. Chen, S. Kaledhonkar, M. Sun, B. Shen, Z. Lu et al., Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy, Structure, vol.23, pp.1097-1105, 2015.

J. Z. Chen, E. C. Settembre, S. T. Aoki, X. Zhang, A. R. Bellamy et al., Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM, Proc. Natl. Acad. Sci. U.S.A, vol.106, pp.10644-10648, 2009.

Y. Chen, S. Pfeffer, J. J. Fernández, C. O. Sorzano, and F. Förster, Autofocused 3D classification of cryoelectron subtomograms, Structure, vol.22, pp.1528-1537, 2014.

E. Y. Chua, V. K. Vogirala, O. Inian, A. S. Wong, L. Nordenskiöld et al., ) 3.9Å structure of the nucleosome core particle determined by phase-plate cryo-EM, Nucleic Acids Res, vol.44, pp.8013-8019, 2016.

W. Dai, C. Fu, H. A. Khant, S. J. Ludtke, M. F. Schmid et al., Zernike phase-contrast electron cryotomography applied to marine cyanobacteria infected with cyanophages, Nat. Protoc, vol.9, pp.2630-2642, 2014.

R. Danev and W. Baumeister, Cryo-EM single particle analysis with the Volta phase plate, Elife, vol.5, p.13046, 2016.

R. Danev, B. Buijsse, M. Khoshouei, J. M. Plitzko, and W. Baumeister, Volta potential phase plate for in-focus phase contrast transmission electron microscopy, Proc. Natl Acad. Sci. U.S.A, vol.44, pp.15635-15640, 2014.

J. Dubochet, M. Adrian, J. J. Chang, J. C. Homo, J. Lepault et al., Cryo-electron microscopy of vitrified specimens, Q. Rev. Biophys, vol.21, pp.129-228, 1988.

A. Dubrovsky, S. Sorrentino, J. Harapin, K. Sapra, T. Medalia et al., Developments in cryo-electron tomography for in situ structural analysis, Arch. Biochem. Biophys, vol.581, pp.78-85, 2015.

N. V. Dudkina, R. Kouril, J. B. Bultema, and E. J. Boekema, Imaging of organelles by electron microscopy reveals protein-protein interactions in mitochondria and chloroplasts, FEBS Lett, vol.584, pp.2510-2515, 2010.

, www.biolcell.net | Volume (109) | Pages, pp.81-93

L. A. Subramaniam and S. , Cryo-EM of viruses and vaccine design, Integrative role of cryo-EM in structural biology Review Earl, vol.113, pp.8903-8905, 2016.

D. Eiler, J. Lin, A. Simonetti, B. P. Klaholz, and T. A. Steitz, IF2 Initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5B and mechanism among translational GTPases, Proc. Nat. Acad. Sci. U.S.A, vol.110, pp.15662-15667, 2013.

P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, Features and development of Coot, Acta Crystallogr. D Biol. Crystallogr, vol.66, pp.486-501, 2010.

N. Fischer, A. L. Konevega, W. Wintermeyer, M. V. Rodnina, and H. Stark, Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy, Nature, vol.466, pp.329-333, 2010.

N. Fischer, P. Neumann, A. L. Konevega, L. V. Bock, R. Ficner et al., Structure of the E. coli ribosome-EF-Tu complex at <3Å resolution by Cs-corrected cryo-EM, Nature, vol.520, pp.567-570, 2015.

A. S. Frangakis, J. Böhm, F. Förster, S. Nickell, D. Nicastro et al., Identification of macromolecular complexes in cryoelectron tomograms of phantom cells, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.14153-14158, 2002.

G. A. Frank, A. Bartesaghi, O. Kuybeda, M. J. Borgnia, T. A. White et al., Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging, J. Struct. Biol, vol.178, pp.165-176, 2012.

N. Frindt, M. Oster, S. Hettler, B. Gamm, L. Dieterle et al., In-focus electrostatic Zach phase plate imaging for transmission electron microscopy with tunable phase contrast of frozen hydrated biological samples, Microsc. Microanal, vol.1, pp.175-183, 2014.

J. Fu, H. Gao, and J. Frank, Unsupervised classification of single particles by cluster tracking in multi-dimensional space, J. Struct. Biol, vol.157, pp.226-239, 2006.

J. G. Galaz-montoya, C. W. Hecksel, P. R. Baldwin, E. Wang, S. C. Weaver et al., Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography, J. Struct. Biol, vol.194, pp.383-394, 2016.

H. Gao, M. Valle, M. Ehrenberg, and J. Frank, Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset, J. Struct. Biol, vol.147, pp.283-290, 2004.

R. M. Glaeser, Protein complexes in focus, Elife, vol.5, 2016.

T. Grant and N. Grigorieff, Measuring the optimal exposure for single particle cryo-EM using a 2.6Å reconstruction of rotavirus VP6, vol.4, p.6980, 2015.

B. J. Greber, P. Bieri, M. Leibundgut, A. Leitner, R. Aebersold et al., The complete structure of the 55S mammalian mitochondrial ribosome, Science, vol.348, pp.303-308, 2015.

C. Hagen, K. C. Dent, T. Zeev-ben-mordehai, M. Grange, J. B. Bosse et al., Cell, vol.163, pp.1692-1701, 2015.

W. J. Hagen, W. Wan, and J. A. Briggs, Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging, J. Struct. Biol, vol.16, pp.30113-30117, 2016.

J. M. Heumann, A. Hoenger, and D. N. Mastronarde, Clustering and variance maps for cryo-electron tomography using wedge-masked differences, J. Struct. Biol, vol.175, pp.288-299, 2011.

R. N. Irobalieva, B. Martins, and O. Medalia, Cellular structural biology as revealed by cryo-electron tomography, J. Cell Sci, vol.129, pp.469-476, 2016.

M. A. Karreman, L. Mercier, N. L. Schieber, G. Solecki, G. Allio et al., Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy, J. Cell Sci, vol.129, pp.444-456, 2016.

H. Khatter, A. G. Myasnikov, L. Mastio, I. M. Billas, C. Birck et al., Purification, characterization and crystallization of the human 80S ribosome, Nucleic Acids Res, vol.42, pp.1-11, 2014.

H. Khatter, A. G. Myasnikov, K. Natchiar, and B. P. Klaholz, Structure of the human 80S ribosome, Nature, vol.520, pp.640-645, 2015.

M. Khoshouei, S. Pfeffer, W. Baumeister, F. Förster, and R. Danev, Subtomogram analysis using the Volta phase plate, J. Struct. Biol, vol.16, pp.30103-30104, 2016.

M. Khoshouei, M. Radjainia, A. J. Phillips, J. A. Gerrard, A. K. Mitra et al., Volta phase plate cryo-EM of the small protein complex Prx3, Nat. Commun, vol.7, p.10534, 2016.

D. Kim, T. J. Deerinck, Y. M. Sigal, H. P. Babcock, M. H. Ellisman et al., Correlative stochastic optical reconstruction microscopy and electron microscopy, PLoS One, vol.10, 2015.

C. Kizilyaprak, J. Daraspe, and B. M. Humbel, Focused ion beam scanning electron microscopy in biology, J. Microsc, vol.254, pp.109-114, 2014.

B. P. Klaholz, Structure sorting of multiple macromolecular states in heterogeneous cryo-EM samples by 3D multivariate statistical analysis, Open J. Stat, vol.5, pp.820-836, 2015.

B. P. Klaholz, A. G. Myasnikov, and M. Van-heel, Visualization of release factor 3 on the ribosome during termination of protein synthesis, Nature, vol.427, pp.862-865, 2004.

R. I. Koning, K. Celler, J. Willemse, E. Bos, G. P. Van-wezel et al., Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces, Methods Cell Biol, vol.124, pp.217-239, 2014.

J. Kosinski, S. Mosalaganti, A. Von-appen, R. Teimer, A. L. Diguilio et al., Molecular architecture of the inner ring scaffold of the human nuclear pore complex, Science, vol.352, pp.363-365, 2016.

M. Kuijper, G. Van-hoften, B. Janssen, R. Geurink, S. De-carlo et al., FEI's direct electron detector developments: Embarking on a revolution in cryo-TEM, J. Struct. Biol, vol.192, pp.179-187, 2015.

W. Kunath, K. Weiss, H. Sack-kongehl, M. Kessel, and E. Zeitler, Time-resolved low-dose microscopy of glutamine synthetase molecules, Ultramicroscopy, vol.13, pp.241-252, 1984.

O. Kuybeda, G. A. Frank, A. Bartesaghi, M. Borgnia, S. Subramaniam et al., Collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography, J. Struct. Biol, vol.181, pp.116-127, 2013.

R. F. Laine, A. Albecka, S. Van-de-linde, E. J. Rees, C. M. Crump et al., Structural analysis of herpes simplex virus by optical super-resolution imaging, Nat. Commun, vol.6, p.5980, 2015.

X. Li, P. Mooney, S. Zheng, C. R. Booth, M. B. Braunfeld et al., Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM, Nat. Methods, vol.10, pp.584-590, 2013.

H. Y. Liao, Y. Hashem, and J. Frank, Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy, Structure, vol.23, pp.1129-1237, 2015.

D. H. Lin, T. Stuwe, S. Schilbach, E. J. Rundlet, T. Perriches et al., , vol.352, p.6283, 2016.

A. Löschberger, C. Franke, G. Krohne, S. Van-de-linde, and M. Sauer, Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution, 2014.

, J. Cell Sci, vol.127, pp.4351-4355

V. Lu?i?, A. Rigort, and W. Baumeister, Cryo-electron tomography: the challenge of doing structural biology in situ, J. Cell Biol, vol.202, pp.407-419, 2013.

D. Lyumkis, A. F. Brilot, D. L. Theobald, and N. Grigorieff, Likelihood-based classification of cryo-EM images using FREALIGN, J. Struct. Biol, vol.183, pp.377-388, 2013.

J. Mahamid, S. Pfeffer, M. Schaffer, E. Villa, R. Danev et al., Visualizing the molecular sociology at the HeLa cell nuclear periphery, Science, vol.351, pp.969-972, 2016.

J. Mahamid, R. Schampers, H. Persoon, A. A. Hyman, W. Baumeister et al., A focused ion beam milling and lift-out approach for site-specific preparation of frozen-hydrated lamellas from multicellular organisms, J. Struct. Biol, vol.192, pp.262-269, 2015.

M. Maletta, I. M. Orlov, P. Roblin, Y. Beck, D. Moras et al., The palindromic DNA-bound USP/EcR nuclear receptor adopts an asymmetric organization with allosteric domain positioning, Nat. Commun, vol.5, p.4139, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02640131

G. Mcmullan, S. Chen, R. Henderson, and A. R. Faruqi, Detective quantum efficiency of electron area detectors in electron microscopy, Ultramicroscopy, vol.109, pp.1126-1143, 2009.

G. Mcmullan, A. R. Faruqi, D. Clare, and R. Henderson, Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy, Ultramicroscopy, vol.147, pp.156-163, 2014.

O. Medalia, I. Weber, A. S. Frangakis, D. Nicastro, G. Gerisch et al., Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography, Science, vol.298, pp.1209-1213, 2002.

J. Ménétret, H. Khatter, A. Simonetti, I. Orlov, A. G. Myasnikov et al., Integrative structure-function analysis of large nucleoprotein complexes, 2013.

A. Merk, A. Bartesaghi, S. Banerjee, V. Falconieri, P. Rao et al., Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery, Cell, vol.165, pp.1698-1707, 2016.

J. L. Milne, M. J. Borgnia, A. Bartesaghi, E. E. Tran, L. A. Earl et al., Cryo-electron microscopy -a primer for the non-microscopist, FEBS J, vol.280, pp.28-45, 2013.

K. Murata, X. Liu, R. Danev, J. Jakana, M. F. Schmid et al., Zernike phase contrast cryo-electron microscopy and tomography for structure determination at nanometer and subnanometer resolutions, Structure, vol.18, pp.903-912, 2010.

A. G. Myasnikov, Z. A. Afonina, J. Ménétret, V. A. Shirokov, A. S. Spirin et al., The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes, Nat. Commun, vol.5, p.5294, 2014.

A. G. Myasnikov, Z. Afonina, and B. P. Klaholz, Single particle and molecular assembly analysis of polyribosomes by single-and double-tilt cryo electron tomography, Ultramicroscopy, vol.126, pp.33-39, 2013.

A. G. Myasnikov, S. K. Natchiar, M. Nebout, I. Hazemann, V. Imbert et al., Structure-function insights reveal the human ribosome as a cancer target for antibiotics, Nat. Commun, vol.7, p.12856, 2016.

A. Nans, M. Kudryashev, H. R. Saibil, and R. D. Hayward, Structure of a bacterial type III secretion system in contact with a host membrane in situ, Nat. Commun, vol.6, p.10114, 2015.

I. Nederlof, Y. W. Li, M. Van-heel, and J. P. Abrahams, Imaging protein three-dimensional nanocrystals with cryo-EM, Acta Crystallogr. D Biol. Crystallogr, vol.69, pp.852-859, 2013.

J. M. Obbineni, R. Yamamoto, and T. Ishikawa, A simple and fast approach for missing-wedge invariant classification of subtomograms extracted from filamentous structures, J. Struct. Biol, vol.16, p.30172, 2016.

I. Orlov, N. Rochel, D. Moras, and B. P. Klaholz, Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA, EMBO J, vol.31, pp.291-300, 2012.

I. Orlov, A. Schertel, G. Zuber, B. P. Klaholz, R. Drillien et al., Live cell immunogold labelling of RNA polymerase II, Sci. Rep, vol.5, p.8324, 2015.

E. V. Orlova and H. R. Saibil, Methods for three-dimensional reconstruction of heterogeneous assemblies, Methods Enzymol, vol.482, pp.321-362, 2010.

J. O. Ortiz, F. Förster, J. Kürner, A. A. Linaroudis, and W. Baumeister, Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition, J. Struct. Biol, vol.156, pp.334-341, 2006.

P. A. Penczek, J. Frank, and C. M. Spahn, A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation, J. Struct. Biol, vol.154, pp.184-194, 2006.

C. Rajendran, F. S. Dworkowski, M. Wang, and C. Schulze-briese, Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector, J. Synchrotron Radiat, vol.18, pp.318-328, 2011.

P. Ray, B. P. Klaholz, R. D. Finn, E. V. Orlova, P. C. Burrows et al., Determination of Escherichia coli RNA polymerase structure by single particle cryoelectron microscopy, Methods Enzymol, vol.370, pp.24-42, 2003.

I. Razinkov, V. P. Dandey, H. Wei, Z. Zhang, D. Melnekoff et al., A new method for vitrifying samples for cryoEM, J. Struct. Biol, vol.195, pp.190-198, 2016.

D. Rhinow, Towards an optimum design for thin film phase plates, Ultramicroscopy, vol.160, pp.1-6, 2016.

A. Rigort and J. M. Plitzko, Cryo-focused-ion-beam applications in structural biology, Arch. Biochem. Biophys, vol.581, pp.122-130, 2015.

R. S. Ruskin, Z. Yu, and N. Grigorieff, Quantitative characterization of electron detectors for transmission electron microscopy, J. Struct. Biol, vol.184, pp.385-393, 2013.

M. R. Sawaya, J. Rodriguez, D. Cascio, M. J. Collazo, D. Shi et al., Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED, Proc. Natl. Acad. Sci. U.S.A, p.201606287, 2016.

M. Schaffer, J. Mahamid, B. D. Engel, T. Laugks, W. Baumeister et al., Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins, J. Struct. Biol, vol.16, pp.30151-30154, 2016.

S. H. Scheres, M. Valle, R. Nuez, C. O. Sorzano, R. Marabini et al., Maximum likelihood multi-reference refinement for electron microscopy images, J. Mol. Biol, vol.22, pp.139-149, 2005.

S. H. Scheres, Classification of structural heterogeneity by maximum-likelihood methods, Methods Enzymol, vol.482, pp.295-320, 2010.

S. H. Scheres, Beam-induced motion correction for sub-megadalton cryo-EM particles, Elife, vol.3, p.3665, 2014.

R. T. Schirra and P. Zhang, Correlative fluorescence and electron microscopy, Curr. Protoc. Cytom, vol.70, pp.1-10, 2014.

M. Schorb, L. Gaechter, O. Avinoam, F. Sieckmann, M. Clarke et al., New hardware and workflows for semi-automated correlative cryo-fluoresence and cryo-electron microscopy/tomography, J. Struct. Biol, vol.16, pp.30135-30136, 2016.

F. K. Schur, M. Obr, W. J. Hagen, W. Wan, A. J. Jakobi et al., An 92 www.biolcell.net | Volume (109) | Pages 81-93 maturation, Science, vol.353, pp.506-508, 2016.

D. Shi, B. L. Nannenga, M. J. De-la-cruz, J. Liu, S. Sawtelle et al., The collection of MicroED data for macromolecular crystallography, Nat. Protoc, vol.11, pp.895-904, 2016.

F. J. Sigworth, A maximum-likelihood approach to single-particle image refinement, J. Struct. Biol, vol.122, pp.328-339, 1998.

A. Simonetti, S. Marzi, A. Fabbretti, I. Hazemann, L. Jenner et al., Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms, Acta Cryst, vol.69, pp.925-933, 2013.

A. Simonetti, S. Marzi, I. M. Billas, A. Tsai, A. Fabbretti et al., Involvement of IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor, Proc. Nat. Acad. Sci. U.S.A, vol.110, pp.15656-15661, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02645085

A. Simonetti, J. Ménétret, F. Martin, A. G. Myasnikov, Q. Vicens et al., , 2016.

, Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation, Nat. Commun, vol.7, p.12622

A. Simonetti, S. Marzi, A. G. Myasnikov, A. Fabbretti, G. Yusupova et al., Structure of the 30S translation initiation complex, Nature, vol.455, pp.416-420, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00342095

O. S. Smart, T. O. Womack, C. Flensburg, P. Keller, W. Paciorek et al., Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER, Acta Crystallogr. D Biol. Crystallogr, vol.68, pp.368-380, 2012.

O. V. Sobolev, P. V. Afonine, P. D. Adams, and A. Urzhumtsev, Programming new geometry restraints: parallelity of atomic groups, J. Appl. Crystallogr, vol.48, pp.1130-1141, 2015.

J. M. Spear, A. J. Noble, Q. Xie, D. R. Sousa, M. S. Chapman et al., The influence of frame alignment with dose compensation on the quality of single particle reconstructions, J. Struct. Biol, vol.192, pp.196-203, 2015.

S. Spinelli, C. Bebeacua, I. Orlov, D. Tremblay, B. P. Klaholz et al., CryoEM structure of the lactococcal siphophage 1358 virion, J. Virol, vol.88, pp.8900-8910, 2014.

M. Stölken, F. Beck, T. Haller, R. Hegerl, I. Gutsche et al., Maximum likelihood based classification of electron tomographic data, J. Struct. Biol, vol.173, pp.77-85, 2011.

A. Szymborska, A. De-marco, N. Daigle, V. C. Cordes, J. A. Briggs et al., Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging, Science, vol.341, pp.655-658, 2013.

Y. Z. Tan, A. Cheng, C. S. Potter, B. Carragher, M. Van-heel et al., Single-particle electron cryo-microscopy: towards atomic resolution, Microscopy (Oxf.), vol.65, pp.307-369, 2000.

D. Veesler, M. G. Campbell, A. Cheng, C. Y. Fu, Z. Murez et al., Maximizing the potential of electron cryomicroscopy data collected using direct detectors, J. Struct. Biol, vol.184, pp.193-202, 2013.

E. Villa, M. Schaffer, J. M. Plitzko, and W. Baumeister, Opening windows into the cell: focused-ion-beam milling for cryo-electron tomography, Curr. Opin. Struct. Biol, vol.23, pp.771-777, 2013.

A. Walter, S. Steltenkamp, S. Schmitz, P. Holik, E. Pakanavicius et al., Towards an optimum design for electrostatic phase plates, Ultramicroscopy, vol.153, pp.22-31, 2015.

W. Wan and J. A. Briggs, Cryo-electron tomography and subtomogram averaging, Methods Enzymol, vol.579, pp.329-367, 2016.

K. Wang, C. Y. Fu, R. Khayat, P. C. Doerschuk, and J. E. Johnson, In vivo virus structures: simultaneous classification, resolution enhancement, and noise reduction in whole-cell electron tomography, J. Struct. Biol, vol.174, pp.425-433, 2011.

H. E. White, H. R. Saibil, A. Ignatiou, and E. V. Orlova, Recognition and separation of single particles with size variation by statistical analysis of their images, J. Mol. Biol, vol.13, pp.453-460, 2004.

W. Wong, X. C. Bai, A. Brown, I. S. Fernandez, E. Hanssen et al., Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. Elife 3, 2014.

M. Xu and F. Alber, Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms, Bioinformatics, vol.29, pp.274-282, 2013.

Z. Yang, K. Lasker, D. Schneidman-duhovny, B. Webb, C. C. Huang et al., UCSF Chimera, MODELLER, and IMP: an integrated modeling system, J. Struct. Biol, vol.179, pp.269-278, 2012.

J. Zhang, G. Ji, X. Huang, W. Xu, and F. Sun, An improved cryo-FIB method for fabrication of frozen hydrated lamella, J. Struct. Biol, vol.194, pp.218-223, 2016.

X. Zhang, P. Ge, X. Yu, J. M. Brannan, G. Bi et al., Cryo-EM structure of the mature dengue virus at 3.5-Å resolution, Nat. Struct. Mol. Biol, vol.20, pp.105-110, 2013.

L. Andronov, Y. Lutz, J. Vonesch, and B. Klaholz, SharpGSDIM, a software for processing of super-resolution microscopy data. Focus on Microscopy-2015, 2015.

L. Andronov, I. Orlov, Y. Lutz, J. Vonesch, and B. Klaholz, ClusterViSu, a method for clustering and colocalization analysis of protein complexes by Voronoi tessellation in single-molecule microscopy, ICON Europe, 2016.

L. Andronov, J. Michalon, K. Ouararhni, I. Orlov, Y. Lutz et al., Segmentation and cluster analysis of protein complexes by Voronoi tessellation in 3D localization microscopy, 2017.