V. Figure, 16: (a,b,c) Maximum intensity orthogonal projections of the fluorescence z-stack. Red circles: the beads positions identified in the fluorescence z-stack

A. Nair, Principles of Biochemistry and Genetic Engineering, 2010.

R. Edmondson, J. J. Broglie, A. F. Adcock, and L. Yang, Three-Dimensional Cell Culture Systems and Their Applications in Drug Discovery and Cell-Based Biosensors, ASSAY and Drug Development Technologies, vol.12, issue.4, pp.207-218, 2014.
DOI : 10.1089/adt.2014.573

F. Pampaloni, E. G. Reynaud, and E. H. Stelzer, The third dimension bridges the gap between cell culture and live tissue, Nature Reviews Molecular Cell Biology, vol.48, issue.10, pp.839-845, 2007.
DOI : 10.1177/002215540004800409

S. Breslin and L. O. Driscoll, Three-dimensional cell culture: the missing link in drug discovery, Drug Discovery Today, vol.18, issue.5-6, pp.240-249, 2013.
DOI : 10.1016/j.drudis.2012.10.003

D. Huh, G. A. Hamilton, and D. E. Ingber, From 3D cell culture to organs-on-chips, Trends in Cell Biology, vol.21, issue.12, pp.745-754, 2011.
DOI : 10.1016/j.tcb.2011.09.005

E. R. Shamir and A. J. Ewald, Three-dimensional organotypic culture: experimental models of mammalian biology and disease, Nature Reviews Molecular Cell Biology, vol.13, issue.10, pp.647-664, 2014.
DOI : 10.1016/j.stem.2013.11.002

M. Ravi, V. Paramesh, S. Kaviya, E. Anuradha, and F. P. Solomon, 3D Cell Culture Systems: Advantages and Applications, Journal of Cellular Physiology, vol.7, issue.1, pp.16-26, 2015.
DOI : 10.1371/journal.pone.0034279

N. Scherf and J. J. Huisken, The smart and gentle microscope, Nature Biotechnology, vol.4, issue.8, 2015.
DOI : 10.1038/nmeth.1175

. Wikipedia, Optical microscope ? Wikipedia The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 19, 2017.

. Wikipedia, Timeline of microscope technology ? Wikipedia, The Free Encyclopedia , " 2017. [Click to open link] [Online; accessed 19, 2017.

Z. Zheng, S. A. Lee, Y. Antebi, M. B. Elowitz, and C. Yang, The ePetri dish, an on-chip cell imaging platform based on subpixel perspective sweeping microscopy (SPSM), Proceedings of the National Academy of Sciences, vol.10, issue.19, pp.16889-16894, 2011.
DOI : 10.1039/c003873c

I. Pushkarsky, Y. Liu, W. Weaver, T. W. Su, O. Mudanyali et al., Automated single-cell motility analysis on a chip using lensfree microscopy, Scientific Reports, vol.7, issue.1, pp.2-14, 2014.
DOI : 10.1109/83.650848

D. Gabor, A New Microscopic Principle, Nature, vol.161, issue.4098, pp.777-778, 1948.
DOI : 10.1038/161777a0

. Wikipedia, ?. Matrigel, and . Wikipedia, The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 10, 2017.

G. Serini, D. Ambrosi, E. Giraudo, A. Gamba, L. Preziosi et al., Modeling the early stages of vascular network assembly, The EMBO Journal, vol.22, issue.8, pp.6-252, 2003.
DOI : 10.1093/emboj/cdg176

F. Pampaloni, E. H. Stelzer, and A. Masotti, Three-Dimensional Tissue Models for Drug Discovery and Toxicology, Recent Patents on Biotechnology, vol.3, issue.2, pp.103-117, 2009.
DOI : 10.2174/187220809788700201

J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross et al., Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies, Science, vol.296, issue.5567, pp.541-545, 2002.
DOI : 10.1126/science.1068206

A. Kak and M. Slaney, Principles of computerized tomographic imaging, 1988.

D. Zhu, K. V. Larin, Q. Luo, and V. V. Tuchin, Recent progress in tissue optical clearing, Laser & Photonics Reviews, vol.8, issue.10, pp.732-757, 2013.
DOI : 10.1002/lapl.201010133

J. F. Colas, J. Sharpe, B. W. Graf, and S. A. Boppart, Live optical projection tomography, Organogenesis, vol.468, issue.4, pp.211-216, 2009.
DOI : 10.1007/978-1-59745-249-6_22
URL : http://www.tandfonline.com/doi/pdf/10.4161/org.5.4.10426?needAccess=true

J. M. Bueno, F. J. Ávila, and P. Artal, Second Harmonic Generation Microscopy: A Tool for Quantitative Analysis of Tissues, Microscopy and Analysis ch. 05, pp.10-11, 2016.
DOI : 10.5772/63493

B. Weigelin, G. J. Bakker, and P. Friedl, Third harmonic generation microscopy of cells and tissue organization, Journal of Cell Science, vol.129, issue.2, pp.245-255, 2016.
DOI : 10.1242/jcs.152272

R. Genthial, E. Beaurepaire, M. C. Schanne-klein, F. Peyrin, D. Farlay et al., Label-free imaging of bone multiscale porosity and interfaces using third-harmonic generation microscopy, Scientific Reports, vol.56, issue.1, p.3419, 2017.
DOI : 10.1002/ar.1092170302
URL : https://hal.archives-ouvertes.fr/hal-01540048

S. T. Hess, T. P. Girirajan, and M. D. Mason, Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy, Biophysical Journal, vol.91, issue.11, pp.4258-4272, 2006.
DOI : 10.1529/biophysj.106.091116
URL : https://doi.org/10.1529/biophysj.106.091116

M. J. Rust, M. Bates, and X. Zhuang, Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM), Nature Methods, vol.127, issue.10, pp.793-796, 2006.
DOI : 10.1038/nmeth929
URL : http://europepmc.org/articles/pmc2700296?pdf=render

S. W. Hell and J. Wichmann, Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy, Optics Letters, vol.19, issue.11, pp.780-782, 1994.
DOI : 10.1364/OL.19.000780

N. Ramanujam, Fluorescence Spectroscopy of Neoplastic and Non-Neoplastic Tissues, Neoplasia, vol.2, issue.1-2, pp.89-117, 2000.
DOI : 10.1038/sj.neo.7900077

F. Pampaloni, B. Chang, and E. H. Stelzer, Light??sheet-based fluorescence microscopy (LSFM) for the quantitative imaging of cells and tissues, Cell and Tissue Research, vol.39, issue.1, pp.129-141, 2015.
DOI : 10.1364/OL.39.003682

P. Y. Liu, L. K. Chin, W. Ser, H. F. Chen, C. M. Hsieh et al., Cell refractive index for cell biology and disease diagnosis: past, present and future, Lab on a Chip, vol.13, issue.4, pp.634-644, 2016.
DOI : 10.1039/C3LC50105A
URL : https://hal.archives-ouvertes.fr/hal-01721076

C. Apelian, F. Harms, O. Thouvenin, and A. C. Boccara, Dynamic full field optical coherence tomography: subcellular metabolic contrast revealed in tissues by interferometric signals temporal analysis, Biomedical Optics Express, vol.7, issue.4, pp.1511-1524, 2016.
DOI : 10.1364/BOE.7.001511

O. Thouvenin, C. Apelian, A. Nahas, M. Fink, and C. Boccara, Full-Field Optical Coherence Tomography as a Diagnosis Tool: Recent Progress with Multimodal Imaging, Applied Sciences, vol.97, issue.3, 2017.
DOI : 10.1364/OE.18.002477

M. Kim, Principles and techniques of digital holographic microscopy, Journal of Photonics for Energy, pp.18005-018005, 2010.
DOI : 10.1117/6.0000006.4

M. Debailleul, B. Simon, V. Georges, O. Haeberlé, and V. Lauer, Holographic microscopy and diffractive microtomography of transparent samples, Measurement Science and Technology, vol.19, issue.7, pp.74009-74022, 2008.
DOI : 10.1088/0957-0233/19/7/074009
URL : https://hal.archives-ouvertes.fr/hal-00869405

B. Simon, M. Debailleul, A. Beghin, Y. Tourneur, and O. Haeberlé, High-resolution tomographic diffractive microscopy of biological samples, Journal of Biophotonics, vol.35, issue.4(10), pp.462-467, 2010.
DOI : 10.1002/jbio.200900094
URL : https://hal.archives-ouvertes.fr/hal-00840301

A. Ali, Y. Abouleila, S. Amer, R. Furushima, S. Emara et al., Quantitative Live Single-cell Mass Spectrometry with Spatial Evaluation by Three-Dimensional Holographic and Tomographic Laser Microscopy, Analytical Sciences, vol.32, issue.2, pp.125-127, 2016.
DOI : 10.2116/analsci.32.125

W. Choi, C. Fang-yen, K. Badizadegan, S. Oh, N. Lue et al., Tomographic phase microscopy, Nature Methods, vol.102, issue.9, pp.717-719, 2007.
DOI : 10.1038/nmeth1078

Y. Sung, W. Choi, C. Fang-yen, K. Badizadegan, R. Dasari et al., Optical diffraction tomography for high resolution live cell imaging, Optics Express, vol.17, issue.1, pp.266-277, 2009.
DOI : 10.1364/OE.17.000266
URL : http://dspace.mit.edu/bitstream/1721.1/51357/1/Submitted%20Version.pdf

O. Haeberlé, K. Belkebir, H. Giovaninni, and A. Sentenac, Tomographic diffractive microscopy: basics, techniques and perspectives, Journal of Modern Optics, vol.92, issue.9, pp.686-699, 2010.
DOI : 10.1126/science.1127344

Y. Cotte, F. Toy, P. Jourdain, N. Pavillon, D. Boss et al., Marker-free phase nanoscopy, Nature Photonics, vol.20, issue.2, pp.113-117, 2013.
DOI : 10.1364/JOSAA.29.000244

L. Tian and L. Waller, 3D intensity and phase imaging from light field measurements in an LED array microscope, Optica, vol.2, issue.2, pp.104-111, 2015.
DOI : 10.1364/OPTICA.2.000104.m002

R. Horstmeyer, J. Chung, X. Ou, G. Zheng, and C. Yang, Diffraction tomography with Fourier ptychography, Optica, vol.3, issue.8, pp.827-835, 2016.
DOI : 10.1364/OPTICA.3.000827.v002
URL : https://authors.library.caltech.edu/70694/1/optica-3-8-827.pdf

M. Chen, L. Tian, and L. Waller, 3D differential phase contrast microscopy, Biomedical Optics Express, vol.7, issue.10, pp.3940-3950, 2016.
DOI : 10.1364/BOE.7.003940.v001
URL : http://europepmc.org/articles/pmc5102530?pdf=render

S. Chowdhury, W. J. Eldridge, A. Wax, and J. A. Izatt, Structured illumination multimodal 3D-resolved quantitative phase and fluorescence sub-diffraction microscopy, Biomedical Optics Express, vol.8, issue.5, pp.2496-2518, 2017.
DOI : 10.1364/BOE.8.002496
URL : http://europepmc.org/articles/pmc5480494?pdf=render

K. Lee, K. Kim, G. Kim, S. Shin, and Y. Park, Time-multiplexed structured illumination using a DMD for optical diffraction tomography, Optics Letters, vol.42, issue.5, pp.999-1002, 2017.
DOI : 10.1364/OL.42.000999

M. E. Dolega, C. Allier, S. V. Kesavan, S. Gerbaud, F. Kermarrec et al., Label-free analysis of prostate acini-like 3D structures by lensfree imaging, Biosensors and Bioelectronics, vol.49, issue.154, pp.176-183, 2013.
DOI : 10.1016/j.bios.2013.05.001

S. V. Kesavan, M. Momey, O. Cioni, B. David-watine, N. Dubrulle et al., High-throughput monitoring of major cell functions by means of lensfree video microscopy, Scientific Reports, vol.199, issue.1, 2014.
DOI : 10.1016/S0030-4018(01)01556-5
URL : https://hal.archives-ouvertes.fr/hal-01385638

L. Denis, C. Fournier, T. Fournel, and C. Ducottet, Twin-image noise reduction by phase retrieval in in-line digital holography, " in Wavelets XI, SPIE's Symposium on Optical Science and Technology, of Proceedings of SPIE ?, pp.59140-59154, 2005.

S. V. Kesavan, F. P. Navarro, M. Menneteau, F. Mittler, B. David-watine et al., Real-time label-free detection of dividing cells by means of lensfree video-microscopy, Journal of Biomedical Optics, vol.19, issue.3, p.36004, 2014.
DOI : 10.1117/1.JBO.19.3.036004.2

R. W. Gerchberg and W. O. Saxton, A practical algorithm for the determination of the phase from image and diffraction plane pictures, Optik, vol.35, issue.20, pp.237-246, 1972.

J. R. Fienup, Phase retrieval algorithms: a comparison, Applied Optics, vol.21, issue.15, pp.2758-2769, 1982.
DOI : 10.1364/AO.21.002758

J. R. Fienup, Reconstruction of an object from the modulus of its Fourier transform, Optics Letters, vol.3, issue.1, pp.27-29, 1978.
DOI : 10.1364/OL.3.000027

Y. Rivenson, Y. Wu, H. Wang, Y. Zhang, A. Feizi et al., Sparsity-based multi-height phase recovery in holographic microscopy, Scientific Reports, vol.54, issue.1, pp.37862-37881, 2016.
DOI : 10.1109/TSP.2006.881199
URL : http://www.nature.com/articles/srep37862.pdf

A. Greenbaum and A. Ozcan, Maskless imaging of dense samples using pixel super-resolution based multi-height lensfree on-chip microscopy, Optics Express, vol.20, issue.3, pp.3129-3143, 2012.
DOI : 10.1364/OE.20.003129

W. Bishara, T. Su, A. F. Coskun, and A. Ozcan, Lensfree on-chip microscopy over a wide field-of-view using pixel super-resolution, Optics Express, vol.18, issue.11, pp.11181-11191, 2010.
DOI : 10.1364/OE.18.011181

J. P. Ryle, S. Mcdonnell, and J. T. Sheridan, Lensless multispectral digital in-line holographic microscope, Journal of Biomedical Optics, vol.16, issue.12, pp.126004-126004, 2011.
DOI : 10.1117/1.3659681

D. W. Noom, D. E. Flaes, E. Labordus, K. S. Eikema, and S. Witte, High-speed multi-wavelength Fresnel diffraction imaging, Optics Express, vol.22, issue.25, pp.30504-30511, 2014.
DOI : 10.1364/OE.22.030504.m003

S. N. Morel, L. Hervé, T. Bordy, O. Cioni, A. Delon et al., Whole slide imaging of unstained tissue using lensfree microscopy, Proceedings SPIE, pp.97111-97111, 2016.

C. Allier, S. Morel, R. Vincent, L. Ghenim, F. Navarro et al., Imaging of dense cell cultures by multiwavelength lens-free video microscopy, Cytometry Part A, vol.211, issue.5, 2017.
DOI : 10.1083/jcb.201505056
URL : https://hal.archives-ouvertes.fr/hal-01480991

S. O. Isikman, W. Bishara, S. Mavandadi, F. W. Yu, S. Feng et al., Lens-free optical tomographic microscope with a large imaging volume on a chip, Proceedings of the National Academy of Sciences, vol.32, issue.1, pp.7296-7301, 2011.
DOI : 10.1364/AO.32.003736

S. O. Isikman, A. Greenbaum, W. Luo, A. F. Coskun, and A. Ozcan, Giga-Pixel Lensfree Holographic Microscopy and Tomography Using Color Image Sensors, PLoS ONE, vol.7, issue.9, pp.45044-45065, 2012.
DOI : 10.1371/journal.pone.0045044.s001
URL : https://doi.org/10.1371/journal.pone.0045044

C. Zuo, J. Sun, J. Zhang, Y. Hu, and Q. Chen, Lensless phase microscopy and diffraction tomography with multi-angle and multi-wavelength illuminations using a LED matrix, Optics Express, vol.23, issue.11, pp.14314-14328, 2015.
DOI : 10.1364/OE.23.014314.m002

E. Wolf, Three-dimensional structure determination of semi-transparent objects from holographic data, Optics Communications, vol.1, issue.4, pp.153-156, 1969.
DOI : 10.1016/0030-4018(69)90052-2

A. J. Devaney, Inverse-scattering theory within the Rytov approximation, Optics Letters, vol.6, issue.8, pp.374-376, 1981.
DOI : 10.1364/OL.6.000374

X. J. Liang, A. Q. Liu, C. S. Lim, T. C. Ayi, and P. H. Yap, Determining refractive index of single living cell using an integrated microchip, Sensors and Actuators A: Physical, vol.133, issue.2, pp.349-354, 2007.
DOI : 10.1016/j.sna.2006.06.045

. Wikipedia, Radon transform ? Wikipedia The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 4, p.35, 2017.

. Wikipedia, Projection-slice theorem ? Wikipedia, The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 4, p.35, 2017.

W. Xu, M. H. Jericho, I. A. Meinertzhagen, and H. J. Kreuzer, Digital in-line holography for biological applications, Proceedings of the National Academy of Sciences, vol.74, issue.11, pp.11301-11305, 2001.
DOI : 10.1016/S0304-3991(98)00036-9

P. Bon, N. Bourg, S. Lecart, S. Monneret, E. Fort et al., Three-dimensional nanometre localization of nanoparticles to enhance super-resolution microscopy, Nature Communications, vol.4, issue.1, p.7764, 2015.
DOI : 10.1364/BOE.4.000885
URL : https://hal.archives-ouvertes.fr/hal-01182402

J. Y. Tinevez, N. Perry, J. Schindelin, G. M. Hoopes, G. D. Reynolds et al., TrackMate: An open and extensible platform for single-particle tracking, Methods, vol.115, issue.185, pp.80-90, 2017.
DOI : 10.1016/j.ymeth.2016.09.016
URL : https://doi.org/10.1016/j.ymeth.2016.09.016

F. Momey, A. Berdeu, T. Bordy, J. Dinten, F. K. Marcel et al., Lensfree diffractive tomography for the imaging of 3D cell cultures, Biomedical Optics Express, vol.7, issue.3, pp.949-962, 2016.
DOI : 10.1364/BOE.7.000949.v008
URL : https://hal.archives-ouvertes.fr/hal-01385606

. Wikipedia, Wiener deconvolution ? Wikipedia The Free Encyclopedia, " 2016. [Click to open link] [Online; accessed 5, p.76, 2017.

. Wikipedia, Fourier transform ? Wikipedia The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 22, p.81, 2017.

M. Schmidt, Limited-memory bfgs, " 2012. [Click to open link] [Online; accessed 22, p.81, 2017.

. Wikipedia, Broyden?Fletcher?Goldfarb?Shanno algorithm ? Wikipedia, The Free Encyclopedia, " 2017. [Online; accessed 6, p.81, 2017.

. Wikipedia, Conic section ? Wikipedia The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 25, p.96, 2017.

T. Visser, J. Oud, and G. Brakenhoff, Refractive index and axial distance measurements in 3-d microscopy, Optik, vol.90, issue.1 2, pp.17-19, 1992.

T. H. Besseling, J. Jose, and A. Van-blaaderen, Methods to calibrate and scale axial distances in confocal microscopy as a function of refractive index, Journal of Microscopy, vol.14, issue.2, pp.142-150, 2015.
DOI : 10.1364/JOSAA.14.001482

A. Berdeu, F. Momey, B. Laperrousaz, T. Bordy, X. Gidrol et al., Comparative study of fully three-dimensional reconstruction algorithms for lens-free microscopy, Applied Optics, vol.56, issue.13, pp.3939-3951, 2017.
DOI : 10.1364/AO.56.003939.v006
URL : https://hal.archives-ouvertes.fr/hal-01561175

A. Berdeu, F. Momey, J. Dinten, X. Gidrol, N. Picollet-d-'hahan et al., Lensfree diffractive tomography for the imaging of 3D cell cultures, Bibliography in Biomedical optics, and imaging conference citations on pages 103 and 221, pp.10070-10070, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01385606

E. Thiébaut, Optimpack library 2017. [Click to open link] [Online; accessed 22, p.118, 2017.

H. Carfantan, Optimpack library interface 2017. [Click to open link] [Online ; accessed 22, p.118, 2017.

D. Krause, P. Vignjevi-?, A. Nassoy, and . Roux, A 3D printed microfluidic device for production of functionalized hydrogel microcapsules for culture and differentiation of human Neuronal Stem Cells (hNSC), Lab on a Chip, vol.16, pp.1593-1604, 2016.

K. Alessandri, B. R. Sarangi, V. V. Gurchenkov, B. Sinha, T. R. Kiessling et al., Cellular capsules as a tool for multicellular spheroid production and for investigating the mechanics of tumor progression in vitro, Proceedings of the National Academy of Sciences, vol.109, issue.3, pp.14843-14848, 2013.
DOI : 10.1073/pnas.1118910109
URL : https://hal.archives-ouvertes.fr/inserm-01356886

M. E. Dolega, F. Abeille, N. Picollet-d-'hahan, and X. Gidrol, Controlled 3D culture in Matrigel microbeads to analyze clonal acinar development, Biomaterials, vol.52, pp.347-357, 2015.
DOI : 10.1016/j.biomaterials.2015.02.042

G. Chen, J. Tang, and S. Leng, Prior image constrained compressed sensing (PICCS): A method to accurately reconstruct dynamic CT images from highly undersampled projection data sets, Medical Physics, vol.34, issue.2, pp.660-663, 2008.
DOI : 10.1118/1.2795830

J. Bailleul, B. Simon, M. Debailleul, H. Liu, and O. Haeberlé, GPU acceleration towards real-time image reconstruction in 3D tomographic diffractive microscopy, Real-Time Image and Video Processing 2012, pp.843707-170, 2012.
DOI : 10.1117/12.922147

X. Liang, B. W. Graf, and S. A. Boppart, Imaging engineered tissues using structural and functional optical coherence tomography, Journal of Biophotonics, vol.13, issue.11, pp.643-655, 2009.
DOI : 10.1148/radiology.157.2.3901109
URL : http://europepmc.org/articles/pmc2883316?pdf=render

S. C. Neves, D. B. Gomes, A. Sousa, S. J. Bidarra, P. Petrini et al., Biofunctionalized pectin hydrogels as 3D cellular microenvironments, Journal of Materials Chemistry B, vol.82, issue.10, pp.2096-2108, 2015.
DOI : 10.1177/154405910308201111
URL : https://re.public.polimi.it/bitstream/11311/971650/1/SaraNeves.pdf

A. Berdeu, F. Momey, B. Laperrousaz, T. Bordy, X. Gidrol et al., 3D lens-free time-lapse microscopy for 3D cell culture, European Conferences on Biomedical Optics, pp.10414-10414, 2017.
DOI : 10.1117/12.2284778

M. L. Gardel, B. Sabass, L. Ji, G. Danuser, U. S. Schwarz et al., Traction stress in focal adhesions correlates biphasically with actin retrograde flow speed, The Journal of Cell Biology, vol.192, issue.6, pp.999-1005, 2008.
DOI : 10.1038/ncb0807-858

. Wikipedia, Full width at half maximum ? Wikipedia, The Free Encyclopedia , " 2016. [Click to open link] [Online; accessed 19, p.203, 2017.

E. Optics, Sensor Relative Illumination, Roll Off and Vignetting, " 2017. [Click to open link] [Online; accessed 01, p.209, 2017.

P. Friedl and K. Wolf, Tumour-cell invasion and migration: diversity and escape mechanisms, Nature Reviews Cancer, vol.3, issue.5, pp.362-374, 2003.
DOI : 10.1038/nrc1075

P. Friedl and D. Gilmour, Collective cell migration in morphogenesis, regeneration and cancer, Nature Reviews Molecular Cell Biology, vol.112, issue.7, pp.445-457, 2009.
DOI : 10.1111/j.1524-475X.2006.00191.x

O. Ilina and P. Friedl, Mechanisms of collective cell migration at a glance, Journal of Cell Science, vol.122, issue.18, pp.3203-3208, 2009.
DOI : 10.1242/jcs.036525

B. Waclaw, I. Bozic, M. E. Pittman, R. H. Hruban, B. Vogelstein et al., A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity, Nature, vol.9, issue.7568, pp.261-264, 2015.
DOI : 10.1088/1478-3975/9/2/026008
URL : http://europepmc.org/articles/pmc4782800?pdf=render

B. Smeets, R. Alert, J. Pe-?-ek, I. Pagonabarraga, H. Ramon et al., Emergent structures and dynamics of cell colonies by contact inhibition of locomotion, Proceedings of the National Academy of Sciences, vol.7, issue.6109, pp.14621-14626, 2016.
DOI : 10.1126/science.aaf6546

P. Friedl, J. Locker, E. Sahai, and J. E. Segall, Classifying collective cancer cell invasion, Nature Cell Biology, vol.129, issue.8, pp.777-783, 2012.
DOI : 10.1002/ijc.26311

A. C. Petrey, C. A. De-la-motte, S. Freitas-rodriguez, A. R. Folgueras, and C. Lopez-otin, The extracellular matrix in IBD, Current Opinion in Gastroenterology, vol.33, issue.4, pp.234-238, 2017.
DOI : 10.1097/MOG.0000000000000368

R. L. Blackmon, R. Sandhu, B. S. Chapman, P. Casbas-hernandez, J. B. Tracy et al., Imaging Extracellular Matrix Remodeling In??Vitro by Diffusion-Sensitive Optical Coherence Tomography, Biophysical Journal, vol.110, issue.8, pp.1858-1868, 2016.
DOI : 10.1016/j.bpj.2016.03.014

B. Lee, J. Konen, S. Wilkinson, A. I. Marcus, and Y. Jiang, Local alignment vectors reveal cancer cell-induced ECM fiber remodeling dynamics, Scientific Reports, vol.11, p.39498, 2017.
DOI : 10.1109/TIP.2002.1014998
URL : http://www.nature.com/articles/srep39498.pdf

Y. Zhang, Y. Shin, K. Sung, S. Yang, H. Chen et al., 3D imaging of optically cleared tissue using a simplified CLARITY method and on-chip microscopy, Science Advances, vol.6, issue.8, 2017.
DOI : 10.1038/srep27811

A. Greenbaum, Y. Zhang, A. Feizi, P. Chung, W. Luo et al., Wide-field computational imaging of pathology slides using lens-free on-chip microscopy, Science Translational Medicine, vol.23, issue.10, pp.267-175, 2014.
DOI : 10.1145/1015706.1015780

F. Soulez, A " learn 2D, apply 3D " method for 3D deconvolution microscopy, 2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI), pp.1075-1078, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00914839

U. S. Kamilov, I. N. Papadopoulos, M. H. Shoreh, A. Goy, C. Vonesch et al., Learning approach to optical tomography, Optica, vol.2, issue.6, pp.517-522, 2015.
DOI : 10.1364/OPTICA.2.000517.s002
URL : http://bigwww.epfl.ch/publications/kamilov1503.pdf

O. Mudanyali, C. Oztoprak, D. Tseng, A. Erlinger, and A. Ozcan, Detection of waterborne parasites using field-portable and cost-effective lensfree microscopy, Lab on a Chip, vol.82, issue.11, pp.2419-2423, 2010.
DOI : 10.3791/1650

R. Eckert, N. Repina, M. Chen, Y. Liang, R. Ng et al., Modeling Light Propagation in 3D Phase Objects, Imaging and Applied Optics 2017 (3D, AIO, COSI, IS, MATH, pcAOP), pp.2-2, 2017.
DOI : 10.1364/3D.2017.DW2F.2

M. Rostykus and C. Moser, Flat Lensless Phase Imager, Imaging and Applied Optics 2016, 2016.
DOI : 10.1364/DH.2016.DM3E.3

M. Rostykus, High resolution flat lensfree phase imager, Digital Holography and Three-Dimensional Imaging, 2017.
DOI : 10.1364/DH.2017.M2A.2

F. Guo, Z. Mao, Y. Chen, Z. Xie, J. P. Lata et al., Three-dimensional manipulation of single cells using surface acoustic waves, Proceedings of the National Academy of Sciences, vol.6, issue.6, pp.1522-1527, 2016.
DOI : 10.1039/c2lc40612h

V. Aubert, R. Wunenburger, T. Valier-brasier, D. Rabaud, J. Kleman et al., A simple acoustofluidic chip for microscale manipulation using evanescent Scholte waves, Lab on a Chip, vol.138, issue.13, pp.2532-2539, 2016.
DOI : 10.1121/1.4922175
URL : https://hal.archives-ouvertes.fr/hal-01339816

K. Kim and Y. Park, Tomographic active optical trapping of arbitrarily shaped objects by exploiting 3D refractive index maps, Nature Communications, vol.9718, p.15340, 2017.
DOI : 10.1117/12.2216769

M. Habaza, M. Kirschbaum, C. Guernth-marschner, G. Dardikman, I. Barnea et al., Rapid 3D Refractive-Index Imaging of Live Cells in Suspension without Labeling Using Dielectrophoretic Cell Rotation, Advanced Science, vol.40, issue.2, p.1600205, 2017.
DOI : 10.1088/0022-3727/40/1/S14

J. M. Soto, J. A. Rodrigo, and T. Alieva, Label-free quantitative 3D tomographic imaging for partially coherent light microscopy, Optics Express, vol.25, issue.14, pp.15699-15712, 2017.
DOI : 10.1364/OE.25.015699.v005

. Wikipedia, Residue theorem ? Wikipedia The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 9, p.229, 2017.

. Wikipedia, Théorème des résidus ? Wikipedia, The Free Encyclopedia, " 2017. [Online; accessed 9, p.229, 2017.

. Wikipedia, Cauchy principal value ? Wikipedia The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 9, p.230, 2017.

L. Houben and M. B. Sadan, Refinement procedure for the image alignment in high-resolution electron tomography, Ultramicroscopy, vol.111, issue.9-10, pp.1512-1520, 2011.
DOI : 10.1016/j.ultramic.2011.06.001

. Wikipedia, Cross-correlation ? Wikipedia The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 1, p.236, 2017.

?. Wikipedia and . Wikipedia, The Free Encyclopedia 2017. [Click to open link] [Online; accessed 1 Least mean squares filter ? Wikipedia, The Free Encyclopedia, 2017.

D. L. Donoho, Compressed sensing, IEEE Transactions on Information Theory, vol.52, issue.4, pp.1289-1306, 2006.
DOI : 10.1109/TIT.2006.871582
URL : https://hal.archives-ouvertes.fr/inria-00369486

L. Denis, D. Lorenz, E. Thiébaut, C. Fournier, and D. Trede, Inline hologram reconstruction with sparsity constraints, Optics Letters, vol.34, issue.22, pp.3475-3477, 2009.
DOI : 10.1364/OL.34.003475
URL : https://hal.archives-ouvertes.fr/ujm-00397994

L. I. Rudin, S. Osher, and E. Fatemi, Nonlinear total variation based noise removal algorithms, Physica D: Nonlinear Phenomena, vol.60, issue.1-4, pp.259-268, 1992.
DOI : 10.1016/0167-2789(92)90242-F

P. Charbonnier, L. Blanc-feraud, G. Aubert, and M. Barlaud, Deterministic edge-preserving regularization in computed imaging, IEEE Transactions on Image Processing, vol.6, issue.2, pp.298-311, 1997.
DOI : 10.1109/83.551699

. Wikipedia, Euler method ? Wikipedia The Free Encyclopedia, " 2017. [Click to open link] [Online; accessed 1, p.252, 2017.

. Wikipedia, Courant?Friedrichs?Lewy condition ? Wikipedia, The Free Encyclopedia , " 2017. [Online; accessed 1, p.256, 2017.