. References-[alberti, Super-resolution microscopy of single atoms in optical lattices, New Journal of Physics, vol.18, p.124, 2016.

A. , Phase shift of a weak coherent beam induced by a single atom, Phys. Rev. Lett, vol.103, p.37, 2009.

P. W. Anderson, More is different, ? Cited on, vol.177, issue.4047, p.1, 1972.

[. Araújo, , 2016.

, Superradiance in a large and dilute cloud of cold atoms in the linear-optics regime, Phys. Rev. Lett, vol.117, p.3

[. Bali, Quantum-diffractive background gas collisions in atom-trap heating and loss, Phys. Rev. A, vol.60, p.94, 1999.

[. Bücker, Single atom sensitive flouresence imaging of ultracold quantum gases, New Journal of Physics, vol.11, p.86, 2009.

[. Bücker, Single-particle-sensitive imaging of freely propagating ultracold atoms, New Journal of Physics, vol.11, issue.10, p.124, 2009.

[. Bender, Observation of cooperative mie scattering from an ultracold atomic cloud, Phys. Rev. A, vol.82, issue.2, p.63822, 2010.

. Bettles, Cooperative ordering in lattices of interacting two-level dipoles, Phys. Rev. A, vol.92, p.104, 2015.

. Bettles, Cooperative eigenmodes and scattering in one-dimensional atomic arrays, Phys. Rev. A, vol.94, p.104, 2016.

. Bettles, Enhanced optical cross section via collective coupling of atomic dipoles in a 2d array, Phys. Rev. Lett, vol.104, issue.116, p.129, 2016.

L. Béguin, Measurement of the van der Waals interaction between two Rydberg atoms, vol.20, p.88, 2013.

[. Bienaimé, Observation of a cooperative radiation force in the presence of disorder, Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light, vol.104, p.77, 2003.

R. Bourgain, Diffusion de la lumière dans les nuages denses mésoscopiques d'atomes froids. PhD thesis, Institut d'Optique Graduate School, p.88, 2014.

[. Bourgain, Direct measurement of the wigner time delay for the scattering of light by a single atom, Opt. Lett, vol.38, issue.11, pp.1963-1965, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01102237

[. Bruno, Maltese cross coupling to individual cold atoms in free space, Optics Express, vol.27, issue.21, p.128, 2019.

[. Campbell, A fermi-degenerate three-dimensional optical lattice clock, Science, vol.358, issue.6359, pp.90-94, 2017.

[. Chabé, Coherent and incoherent multiple scattering, Phys. Rev. A, vol.89, issue.2, p.43833, 2014.

[. References and . Chalony, Coherent flash of light emitted by a cold atomic cloud, Phys. Rev. A, vol.84, issue.2, p.11401, 2011.

[. Chang, Controlling dipoledipole frequency shifts in a lattice-based optical atomic clock, Phys. Rev. A, vol.69, issue.2, p.23810, 2004.

. Cohen-tannoudji, Mécanique quantique. EDP science, p.26, 2018.

J. Dalibard, Cours collège de france, 2013.

B. Darquié, Manipulation d'atomes dans des pièges dipolaires microscopiques et émission contrôlée de photons par un atome unique, p.10, 2005.

R. H. Dicke, Coherence in spontaneous radiation processes, Phys. Rev, vol.93, p.33, 1954.

[. Durant, Light scattering by a random distribution of particles embedded in absorbing media: full-wave monte carlo solutions of the extinction coefficient, J. Opt. Soc. Am. A, vol.24, issue.9, p.29, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01630446

[. Eng, Transcriptome-scale super-resolved imaging in tissues by rna seqfish+, Nature, vol.568, p.119, 2019.

[. Engler, Very long storage times and evaporative cooling of cesium atoms in a quasielectrostatic dipole trap, Phys. Rev. A, vol.62, p.89, 2000.

[. Feynman, Mainly electromagnetism and matter, vol.2, p.3, 1965.

C. E. Floyd, An artificial neural network for spect image reconstruction, IEEE Transactions on Medical Imaging, vol.10, issue.3, p.119, 1991.

C. J. Foot, Atomic physics, vol.7, p.1, 2005.

[. References and . Friedberg, Frequency shift and absorption by resonant systems of two-level atoms, Physics Reports, vol.7, p.43, 1973.

A. Fuhrmanek, From single to many atoms in a microscopic optical dipole trap, vol.14, p.88, 2011.
URL : https://hal.archives-ouvertes.fr/tel-00655970

[. Gillen, Analytical beam propagation model for clipped focused-gaussian beams using vector diffraction theory, Optics Express, vol.18, p.101, 2010.

[. Grynberg, Introduction to Quantum Optics -From the semi-classical approach to Quantized Light, vol.8, p.46, 2010.

[. Huang, Mode imaging and selection in strongly coupled nanoantennas, Nano Letters, vol.10, issue.6, p.1, 2010.

[. Huntemann, Single-ion atomic clock with 3 × 10 ?18 systematic uncertainty, Phys. Rev. Lett, vol.116, p.1, 2016.

[. Iakoupov, Dispersion relations for stationary light in one-dimensional atomic ensembles, Phys. Rev. A, vol.94, p.104, 2016.

J. D. Jackson, Classical Electrodynamics. John Wiley and Sons, vol.26, p.43, 1999.

[. Javanainen, One-dimensional modeling of light propagation in dense and degenerate samples, Phys. Rev. A, vol.59, p.27, 1999.

. Jenkins, Collective resonance fluorescence in small and dense atom clouds: Comparison between theory and experiment, Phys. Rev. A, vol.94, p.45, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01688964

S. Jennewein, Optical Response of dense 87 Rb clouds, vol.57, p.128, 2017.
URL : https://hal.archives-ouvertes.fr/tel-01547493

. References-[jennewein, Coherent scattering of near-resonant light by a dense microscopic cold atomic cloud, Phys. Rev. Lett, vol.116, p.127, 2016.

[. Jennewein, Coherent scattering of near-resonant light by a dense, microscopic cloud of cold two-level atoms: Experiment versus theory, Phys. Rev. A, vol.97, p.127, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02407782

. Keaveney, Maximal refraction and superluminal propagation in a gaseous nanolayer, Phys. Rev. Lett, vol.109, p.127, 2012.

[. Kuhr, Deterministic delivery of a single atom, Science, vol.293, p.86, 2001.

S. Kuraptsev, A. Kuraptsev, and I. Sokolov, Influence of atomic motion on the collective effects in dense and cold atomic ensembles, p.128, 2019.

[. Kwong, Cooperative emission of a pulse train in an optically thick scattering medium, Phys. Rev. Lett, vol.115, p.3, 2015.

[. Kwong, Cooperative emission of a coherent superflash of light, Phys. Rev. Lett, vol.113, issue.2, p.223601, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00994145

[. Lett, Observation of atoms laser cooled below the doppler limit, Phys. Rev. Lett, vol.61, p.17, 1988.

[. Li, Spectrum of collective spontaneous emission beyond the rotating-wave approximation, Phys. Rev. A, vol.87, p.33, 2013.

[. Lubeck, E. Long-;-lubeck, and C. Long, Single-cell systems biology by super-resolution imaging and combinatorial labeling, Nature methods, vol.9, issue.7, p.119, 2012.

J. Manassah, Cooperative radiation from atoms in different geometries: decay rate and frequency shift, Adv. Opt. Photon, vol.4, p.43, 2012.

[. References and . Marti, Imaging optical frequencies with 100 µHz precision and 1.1 µm resolution, Phys. Rev. Lett, vol.120, issue.2, p.103201, 2018.

[. Mølmer, Monte carlo wave-function method in quantum optics, J. Opt. Soc. Am. B, vol.10, issue.3, p.111, 1993.

[. Munro, Population mixing due to dipole-dipole interactions in a one-dimensional array of multilevel atoms, Phys. Rev. A, vol.98, p.104, 2018.

. Nelson, Imaging single atoms in a three-dimensional array, Nature Physics, vol.3, p.86, 2007.

[. Ozeri, Hyperfine coherence in the presence of spontaneous photon scattering, Phys. Rev. Lett, vol.95, p.11, 2005.

[. Pellegrino, Observation of suppression of light scattering induced by dipole-dipole interactions in a cold-atom ensemble, Phys. Rev. Lett, vol.113, p.127, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00949944

. Perczel, Topological quantum optics in two-dimensional atomic arrays, Phys. Rev. Lett, vol.119, issue.2, p.23603, 2017.

[. Peyrot, Fabrication and characterization of super-polished wedged borosilicate nano-cells, Opt. Lett, vol.44, issue.8, p.3, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02140514

[. Peyrot, Measurement of the atom-surface van der waals interaction by transmission spectroscopy in a wedged nano-cell, Physical Review A. ? Cited, vol.3, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02140513

[. Peyrot, Collective lamb shift of a nanoscale atomic vapor layer within a sapphire cavity, Phys. Rev. Lett, vol.120, p.3, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02140519

[. References and . Peyrot, Optical transmission of an atomic vapor in the mesoscopic regime, Phys. Rev. Lett, vol.122, p.3, 2019.

M. Phillips, W. Phillips, and H. Metcalf, Laser deceleration of an atomic beam, Phys. Rev. Lett, vol.48, p.15, 1982.

. Pu, J. Zhang-;-pu, and H. Zhang, Intensity distribution of gaussian beams focused by a lens with spherical aberration, Optics Communications, vol.151, p.96, 1998.

R. Rashed, A pioneer in anaclastics: Ibn sahl on burning mirrors and lenses, Isis, vol.81, issue.3, p.1, 1990.

[. Roof, Observation of single-photon superradiance and the cooperative lamb shift in an extended sample of cold atoms, Phys. Rev. Lett, vol.117, p.3, 2016.

[. Schilder, Role of polaritonic modes on light scattering from a dense cloud of atoms, Phys. Rev. A, vol.93, p.51, 2016.

[. Schlosser, Collisional blockade in microscopic optical dipole traps, Phys. Rev. Lett, vol.89, p.20, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00554211

[. Schlosser, Subpoissonian loading of a microscopic dipole trap, Nature, vol.411, p.86, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00554215

M. O. Scully, Collective lamb shift in single photon dicke superradiance, Phys. Rev. Lett, vol.102, p.33, 2009.

[. Shahmoon, Cooperative resonances in light scattering from two-dimensional atomic arrays, Phys. Rev. Lett, vol.118, issue.2, p.113601, 2017.

[. Shahmoon, Cooperative resonances in light scattering from two-dimensional atomic arrays, Phys. Rev. Lett, vol.118, p.129, 2017.

[. Sherson, Single-atom-resolved fluorescence imaging of an atomic mott insulator, Nature, vol.467, p.124, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01397842

. Sortais, Diffraction-limited optics for single-atom manipulation, Phys. Rev. A, vol.75, p.56, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00509083

D. A. Steck, Rubidium 87 D line data, vol.47, p.137, 2015.

[. Sutherland, R. T. Sutherland, and F. Robicheaux, Collective dipole-dipole interactions in an atomic array, 94:013847. ? Cited on pages 5, vol.104, p.128, 2016.

. Tey, Interfacing light and single atoms with a lens, New Journal of Physics, vol.11, p.42, 2009.

[. Ville, Loading and compression of a single two-dimensional bose gas in an optical accordion, Phys. Rev. A, vol.95, p.101, 2017.

D. J. Wales, Energy Landscapes, p.122, 2003.
URL : https://hal.archives-ouvertes.fr/hal-01423280

D. Wales, D. J. Wales, and J. P. Doye, Global optimization by basin-hopping and the lowest energy structures of lennard-jones clusters containing up to 110 atoms, The Journal of Physical Chemistry A, vol.101, issue.28, p.122, 1997.

S. Wales, D. J. Wales, and H. A. Scheraga, Global optimization of clusters, crystals, and biomolecules, Science, vol.285, issue.5432, p.122, 1999.

[. Weiss, Robustness of dicke subradiance against thermal decoherence, Phys. Rev. A, vol.100, p.128, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02389191

[. Zhu, Image reconstruction by domain-transform manifold learning, Nature, vol.555, p.119, 2018.