Z. Wang, L. Liu, Y. Wang, N. Xi, Z. Dong et al., Automated System for Measuring Cellular Mechanical Properties, J. Lab. Autom, vol.2012, issue.6, pp.443-448

R. Roy, W. Chen, L. Cong, L. A. Goodell, D. J. Foran et al., A Semi-Automated Positioning System for Contact-Mode Atomic Force Microscopy (AFM)

. Autom, . Sci, and . Eng, , vol.10, pp.462-465, 2013.

M. Favre, J. Polesel-maris, T. Overstolz, P. Niedermann, S. Dasen et al., Parallel AFM Imaging and Force Spectroscopy Using Two-Dimensional Probe Arrays for Applications in Cell Biology, J. Mol. Recognit, vol.24, issue.3, pp.446-452, 2011.

A. Dujardin, P. D. Wolf, F. Lafont, and V. Dupres, Automated Multi-Sample Acquisition and Analysis Using Atomic Force Microscopy for Biomedical Applications, PLOS ONE, vol.2019, issue.3
URL : https://hal.archives-ouvertes.fr/inserm-02229466

G. Binnig, H. Rohrer, C. Gerber, and E. Weibel, Surface Studies by Scanning Tunneling Microscopy, Phys. Rev. Lett, vol.1982, issue.1, pp.57-61

L. A. Bottomley, E. D. Gadsby, and M. A. Poggi, MICROSCOPY TECHNIQUES | Atomic Force and Scanning Tunneling Microscopy, Encyclopedia of Analytical Science

P. Worsfold, A. Townshend, and C. Poole, , pp.143-151, 2005.

M. C. Piontek and W. H. Roos, Atomic Force Microscopy: An Introduction, Single Molecule Analysis: Methods and Protocols

, , pp.243-258, 2018.

C. Formosa and E. Dague, Imaging Living Yeast Cells and Quantifying Their Biophysical Properties by Atomic Force Microscopy, Advanced Microscopy in Mycology

T. E. Dahms and K. J. Czymmek, Fungal Biology, pp.125-141, 2015.

A. J. Malkin, T. A. Land, Y. G. Kuznetsov, A. Mcpherson, and J. J. Deyoreo, Investigation of Virus Crystal Growth Mechanisms by In Situ Atomic Force Microscopy, Phys. Rev. Lett, issue.14, pp.2778-2781, 1995.

M. Rief, M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub, Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM, Science, vol.276, issue.5315, pp.1109-1112, 1997.

N. J. Tao, S. M. Lindsay, and S. Lees, Measuring the Microelastic Properties of Biological Material, Biophys. J, vol.63, issue.4, pp.1165-1169, 1992.

A. Meister, M. Gabi, P. Behr, P. Studer, J. Vörös et al., Combining Atomic Force Microscopy and Nanofluidics in a Universal Liquid Delivery System for Single Cell Applications and Beyond, Nano Lett, vol.9, issue.6, pp.2501-2507, 2009.

T. Ando, N. Kodera, E. Takai, D. Maruyama, K. Saito et al., A High-Speed Atomic Force Microscope for Studying Biological Macromolecules, Proc. Natl. Acad. Sci, vol.98, pp.12468-12472, 2001.

A. Syahir, K. Usui, K. Tomizaki, K. Kajikawa, and H. Mihara, Label and Label-Free Detection Techniques for Protein Microarrays, vol.4, pp.228-244, 2015.

M. Lekka, P. Laidler, D. Gil, J. Lekki, Z. Stachura et al., Elasticity of Normal and Cancerous Human Bladder Cells Studied by Scanning Force Microscopy, Eur. Biophys. J, vol.28, issue.4, pp.312-316, 1999.

S. E. Cross, Y. Jin, J. Rao, and J. Gimzewski, Nanomechanical Analysis of Cells from Cancer Patients, Nat. Nanotechnol, vol.2, issue.12, pp.780-783, 2007.

,

R. Omidvar, M. Tafazzoli-shadpour, M. A. Shokrgozar, and M. Rostami, Atomic Force Microscope-Based Single Cell Force Spectroscopy of Breast Cancer Cell Lines: An Approach for Evaluating Cellular Invasion, J. Biomech, vol.47, issue.13, pp.3373-3379, 2014.

L. Bastatas, D. Martinez-marin, J. Matthews, J. Hashem, Y. J. Lee et al., AFM Nano-Mechanics and Calcium Dynamics of Prostate Cancer Cells with Distinct Metastatic Potential, Biochim. Biophys. Acta BBA -Gen. Subj, vol.2012, issue.7, pp.1111-1120

G. Smolyakov, B. Thiebot, C. Campillo, S. Labdi, C. Severac et al., Adhesion, and Tether Extrusion on Breast Cancer Cells Provide a Signature of Their Invasive Potential, ACS Appl. Mater. Interfaces, vol.8, issue.41, pp.27426-27431, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01552762

M. Lekka, M. Fornal, G. Pyka-fo?ciak, K. Lebed, B. Wizner et al., Erythrocyte Stiffness Probed Using Atomic Force Microscope, Biorheology, vol.42, issue.4, pp.307-317, 2005.

I. Duli?ska, M. Targosz, W. Strojny, M. Lekka, P. Czuba et al., Stiffness of Normal and Pathological Erythrocytes Studied by Means of Atomic Force Microscopy, J. Biochem. Biophys. Methods, vol.66, issue.1, pp.1-11, 2006.

,

J. C. Benech, N. Benech, A. I. Zambrana, I. Rauschert, V. Bervejillo et al., Diabetes Increases Stiffness of Live Cardiomyocytes Measured by Atomic Force Microscopy Nanoindentation, Am. J. Physiol.-Cell Physiol, vol.307, issue.10, pp.910-919, 2014.

E. Dague, G. Genet, V. Lachaize, C. Guilbeau-frugier, J. Fauconnier et al., Atomic Force and Electron Microscopic-Based Study of Sarcolemmal Surface of Living Cardiomyocytes Unveils Unexpected Mitochondrial Shift in Heart Failure, J. Mol. Cell. Cardiol, vol.74, pp.162-172, 2014.
URL : https://hal.archives-ouvertes.fr/inserm-01016102

P. C. Braga and D. Ricci, Differences in the Susceptibility of Streptococcus Pyogenes to Rokitamycin and Erythromycin A Revealed by Morphostructural Atomic Force Microscopy

, J. Antimicrob. Chemother, vol.50, issue.4, pp.457-460, 2002.

C. Formosa, M. Grare, R. E. Duval, and E. Dague, Nanoscale Effects of Antibiotics on P. Aeruginosa. Nanomedicine Nanotechnol. Biol. Med, vol.2012, issue.1, pp.12-16

N. Wang, J. P. Butler, and D. E. Ingber, Mechanotransduction across the Cell Surface and through the Cytoskeleton, Science, vol.260, issue.5111, pp.1124-1127, 1993.

, , pp.301-326

,

P. Panorchan, J. S. Lee, B. R. Daniels, T. P. Kole, Y. Tseng et al., Probing Cellular Mechanical Responses to Stimuli Using Ballistic Intracellular Nanorheology, In Methods in Cell Biology, vol.83, pp.113-140, 2007.

K. K. Chu, D. Mojahed, C. M. Fernandez, Y. Li, L. Liu et al., Particle-Tracking Microrheology Using Micro-Optical Coherence Tomography, Biophys. J, vol.111, issue.5, pp.1053-1063, 2016.

M. Gómez-gonzález, One-and Two-Point Particle Tracking Microrheology of Complex Viscoelastic Fluids, 2015.

O. Thoumine and A. Ott, Time Scale Dependent Viscoelastic and Contractile Regimes in Fibroblasts Probed by Microplate Manipulation, J. Cell Sci, vol.110, issue.17, pp.2109-2116, 1997.

L. H. Hellström, M. A. Samaha, K. M. Wang, A. J. Smits, and M. Hultmark, Errors in Parallel-Plate and Cone-Plate Rheometer Measurements Due to Sample Underfill, Meas. Sci. Technol, vol.26, issue.1, p.15301, 2014.

P. Fernández, L. Heymann, A. Ott, N. Aksel, and P. A. Pullarkat, Shear Rheology of a Cell Monolayer, New J. Phys, vol.9, issue.11, pp.419-419, 2007.

J. Guck, R. Ananthakrishnan, H. Mahmood, T. J. Moon, C. C. Cunningham et al., The Optical Stretcher: A Novel Laser Tool to Micromanipulate Cells, Biophys. J, vol.81, issue.2, pp.767-784, 2001.

J. Guck, S. Schinkinger, B. Lincoln, F. Wottawah, S. Ebert et al., Optical Deformability as an Inherent Cell Marker for Testing Malignant Transformation and Metastatic Competence, Biophys. J, vol.88, issue.5, pp.3689-3698, 2005.

T. Yang, F. Bragheri, and P. Minzioni, A Comprehensive Review of Optical Stretcher for Cell Mechanical Characterization at Single-Cell Level. Micromachines, vol.7, p.90, 2016.

D. D. Carlo, A Mechanical Biomarker of Cell State in Medicine, J. Lab. Autom, vol.2012, issue.1, pp.32-42

Z. Wang, L. Liu, Y. Wang, N. Xi, Z. Dong et al., Automated System for Measuring Cellular Mechanical Properties, J. Lab. Autom, vol.2012, issue.6, pp.443-448

R. Roy, W. Chen, L. Cong, L. A. Goodell, D. J. Foran et al., A Semi-Automated Positioning System for Contact-Mode Atomic Force Microscopy (AFM)

. Autom, . Sci, and . Eng, , vol.10, pp.462-465, 2013.

M. Favre, J. Polesel-maris, T. Overstolz, P. Niedermann, S. Dasen et al., Parallel AFM Imaging and Force Spectroscopy Using Two-Dimensional Probe Arrays for Applications in Cell Biology, J. Mol. Recognit, vol.24, issue.3, pp.446-452, 2011.

H. Sadeghian, R. Herfst, B. Dekker, J. Winters, T. Bijnagte et al., High-Throughput Atomic Force Microscopes Operating in Parallel, Rev. Sci. Instrum, vol.2017, issue.3, p.33703

A. Dujardin, P. D. Wolf, F. Lafont, and V. Dupres, Automated Multi-Sample Acquisition and Analysis Using Atomic Force Microscopy for Biomedical Applications, PLOS ONE, vol.2019, issue.3
URL : https://hal.archives-ouvertes.fr/inserm-02229466

A. Martínez-rivas, E. Dague, S. Proa-coronado, C. Séverac, and G. González-quijano, Process by Atomic Force Microscopy for the Massive Physical and Mechanical Analysis of Materials, arrays and structures of biomaterials

D. Etienne,

P. Coronado and S. ,

A. Martinez-rivas, AUTOMATIP: Automation of Biophysical Measurements on Cells by Atomic Force Microscope (AFM

N. Instituto-politecnico, , 2017.

C. Formosa, F. Pillet, M. Schiavone, R. E. Duval, L. Ressier et al., Generation of Living Cell Arrays for Atomic Force Microscopy Studies, Nat. Protoc, vol.10, issue.1, pp.199-204, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01495201

C. Formosa, M. Schiavone, H. Martin-yken, J. M. François, R. E. Duval et al., Nanoscale Effects of Caspofungin against Two Yeast Species, Saccharomyces Cerevisiae and Candida Albicans, Antimicrob. Agents Chemother, vol.2013, issue.8, pp.3498-3506
URL : https://hal.archives-ouvertes.fr/hal-02937573

O. Heinisch and W. G. Cochran, Sampling Techniques, 2. Aufl, Biom. Z, vol.7, issue.3, pp.203-203, 1963.

,

T. Yamane, Statistics: An Introductory Analysis

&. Harper and . Row, , 1967.

S. El-kirat-chatel, A. Beaussart, D. Alsteens, D. N. Jackson, P. N. Lipke et al., Nanoscale Analysis of Caspofungin-Induced Cell Surface Remodelling in Candida Albicans, Nanoscale, vol.2013, issue.3, pp.1105-1115

T. M. Press, Machine Learning, 2019.

J. F. Mccarthy, K. A. Marx, P. E. Hoffman, A. G. Gee, P. O'neil et al., Applications of Machine Learning and High-Dimensional Visualization in Cancer Detection, Diagnosis, and Management, Ann. N. Y. Acad. Sci, vol.1020, issue.1, pp.239-262, 2004.

E. Dague, R. Bitar, H. Ranchon, F. Durand, H. M. Yken et al., An Atomic Force Microscopy Analysis of Yeast Mutants Defective in Cell Wall Architecture, Yeast, vol.2010, issue.8, pp.673-684
URL : https://hal.archives-ouvertes.fr/hal-02937501

D. C. Poulain and . Albicans, Plasticity and Pathogenesis, Crit. Rev. Microbiol, vol.41, issue.2, pp.208-217, 2015.

G. Hwang, Y. Liu, D. Kim, Y. Li, D. J. Krysan et al., Candida Albicans Mannans Mediate Streptococcus Mutans Exoenzyme GtfB Binding to Modulate Cross-Kingdom Biofilm Development in Vivo, PLOS Pathog, vol.13, issue.6, 2017.

E. Dague, E. Jauvert, L. Laplatine, B. Viallet, C. Thibault et al., Assembly of Live Micro-Organisms on Microstructured PDMS Stamps by Convective/Capillary Deposition for AFM Bio-Experiments, Nanotechnology, vol.22, issue.39, p.395102, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01767584

J. J. Harrison, R. J. Turner, and H. Ceri, A Subpopulation of Candida Albicans and Candida Tropicalis Biofilm Cells Are Highly Tolerant to Chelating Agents, FEMS Microbiol. Lett, issue.2, pp.172-181, 2007.

P. D. Khot, P. A. Suci, R. L. Miller, R. D. Nelson, and B. J. Tyler, A Small Subpopulation of Blastospores in Candida Albicans Biofilms Exhibit Resistance to Amphotericin B Associated with Differential Regulation of Ergosterol and ?-1,6-Glucan Pathway Genes, Antimicrob. Agents Chemother, vol.50, issue.11, pp.3708-3716, 2006.

M. Schiavone, S. Déjean, N. Sieczkowski, M. Castex, E. Dague et al., Integration of Biochemical, Biophysical and Transcriptomics Data for Investigating the Structural and Nanomechanical Properties of the, Yeast Cell Wall. Front. Microbiol, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01698344

A. Rosenberg, I. V. Ene, M. Bibi, S. Zakin, E. S. Segal et al., Antifungal Tolerance Is a Subpopulation Effect Distinct from Resistance and Is Associated with Persistent Candidemia, Nat. Commun, vol.9, issue.1, p.2470, 2018.

P. W. Groot and . De,

O. Bader, A. D. Boer, M. Weig, and N. Chauhan, Adhesins in Human Fungal Pathogens: Glue with Plenty of Stick, Eukaryot. Cell, vol.12, issue.4, pp.470-481, 2013.

P. Sajeesh, A. Raj, M. Doble, and A. K. Sen, Characterization and Sorting of Cells Based on Stiffness Contrast in a Microfluidic Channel, RSC Adv, vol.2016, issue.78, pp.74704-74714

K. B. Tománková, P. Kolar, J. Malohlava, and H. Kolá?ová, Mechanical Characterisation of HeLa Cells Using Atomic Force Microscopy, 2012.

A. Martinez-rivas and G. K. González-quijano, Micro and nanoengineering advances for the development and commercialization of organ-on-chips, Biol. Eng. Med, vol.2, issue.2, 2017.

V. S. Shirure and S. C. George, Design considerations to minimize the impact of drug absorption in polymer-based organ-on-a-chip platforms, Lab Chip, vol.17, pp.681-690, 2017.

B. R. Ware, D. R. Berger, and S. R. Khetani, Prediction of Drug-Induced Liver Injury in Micropatterned Co-cultures Containing iPSC-Derived Human Hepatocytes, Toxicol. Sci, vol.145, pp.252-262, 2015.

L. M. Griep, F. Wolbers, B. De-wagenaar, P. M. Ter-braak, B. B. Weksler et al., BBB on chip: Microfluidic platform to mechanically and biochemically modulate blood-brain barrier function, Biomed. Microdevices, vol.15, pp.145-150, 2013.

J. Zhao, Y. Cao, L. A. Dipietro, and J. Liang, Dynamic cellular finite-element method for modelling large-scale cell migration and proliferation under the control of mechanical and biochemical cues: A study of re-epithelialization, J. R. Soc. Interface, vol.14, 2017.

D. T. Phan, R. H. Bender, J. W. Andrejecsk, A. Sobrino, S. J. Hachey et al., Blood-brain barrier-on-a-chip: Microphysiological systems that capture the complexity of the blood-central nervous system interface, Exp. Biol. Med, vol.242, pp.1669-1678, 2017.

D. Huh, B. D. Matthews, A. Mammoto, M. Montoya-zavala, H. Y. Hsin et al., Reconstituting Organ-Level Lung Functions on a Chip, Science, vol.328, pp.1662-1668, 2010.

N. Beißner, T. Lorenz, and S. Reichl, Chapter 11: Organ on chip, Microsystems for Pharmatechnology: Manipulation of Fluids, Particles, Droplets, and Cells

A. Dietzel, . Ed, and . Springer, , pp.299-339, 2016.

B. Städler, D. Falconnet, I. Pfeiffer, F. Höök, and J. Vörös, Micropatterning of DNA-Tagged Vesicles, Langmuir, vol.20, pp.11348-11354, 2004.

R. Estevam-alves, P. H. Ferreira, A. C. Coatrini, O. N. Oliveira, C. R. Fontana et al., Femtosecond Laser Patterning of the Biopolymer Chitosan for Biofilm Formation, Int. J. Mol. Sci, vol.17, 1243.

G. Huang, Y. Mei, D. J. Thurmer, E. Coric, and O. G. Schmidt, Rolled-up transparent microtubes as two-dimensionally confined culture scaffolds of individual yeast cells, Lab Chip, vol.9, pp.263-268, 2009.

C. Credi, C. De-marco, E. Molena, M. Pla-roca, J. Samitier-martí et al., Heparin micropatterning onto fouling-release perfluoropolyether-based polymers via photobiotin activation, Colloids Surf. B Biointerfaces, vol.146, pp.250-259, 2016.

P. Gascoyne, C. Mahidol, M. Ruchirawat, J. Satayavivad, P. Watcharasit et al., Microsample preparation by dielectrophoresis: Isolation of malaria, Lab Chip, vol.2, pp.70-75, 2002.

Y. Lee, H. J. Lee, K. Jin-son, and W. Koh, Fabrication of hydrogel-micropatterned nanofibers for highly sensitive microarray-based immunosensors having additional enzyme-based sensing capability, J. Mater. Chem, vol.21, pp.4476-4483, 2011.

C. Formosa, F. Pillet, M. Schiavone, R. E. Duval, L. Ressier et al., Generation of living cell arrays for atomic force microscopy studies, Nat. Protoc, vol.10, pp.199-204, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01495201

Y. Imamura, T. Mukohara, Y. Shimono, Y. Funakoshi, N. Chayahara et al., Comparison of 2D-and 3D-culture models as drug-testing platforms in breast cancer, Oncol. Rep, vol.33, pp.1837-1843, 2015.

R. Langer and D. A. Tirrell, Designing materials for biology and medicine, Nature, vol.428, pp.487-492, 2004.

L. D'amico, N. J. Ajami, J. A. Adachi, P. R. Gascoyne, and J. F. Petrosino, Isolation and concentration of bacteria from blood using microfluidic membraneless dialysis and dielectrophoresis, Lab Chip, vol.17, pp.1340-1348, 2017.

K. Ino, A. Ito, and H. Honda, Cell patterning using magnetite nanoparticles and magnetic force, Biotechnol. Bioeng, vol.97, pp.1309-1317, 2007.

G. R. Souza, H. Tseng, J. A. Gage, A. Mani, P. Desai et al., Magnetically Bioprinted Human Myometrial 3D Cell Rings as A Model for Uterine Contractility, Int. J. Mol. Sci, vol.18, 2017.

J. Pivetal, D. Royet, G. Ciuta, M. Frenea-robin, N. Haddour et al., Micro-magnet arrays for specific single bacterial cell positioning, J. Magn. Magn. Mater, vol.380, pp.72-77, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01113985

S. C. Wei, L. Fattet, J. H. Tsai, Y. Guo, V. H. Pai et al., Matrix stiffness drives epithelial-mesenchymal transition and tumour metastasis through a TWIST1-G3BP2 mechanotransduction pathway, Nat. Cell Biol, vol.17, pp.678-688, 2015.

M. Kwon, S. A. Godinho, N. S. Chandhok, N. J. Ganem, A. Azioune et al., Mechanisms to suppress multipolar divisions in cancer cells with extra centrosomes, Genes Dev, vol.22, pp.2189-2203, 2008.

M. Théry, V. Racine, M. Piel, A. Pépin, A. Dimitrov et al., Anisotropy of cell adhesive microenvironment governs cell internal organization and orientation of polarity, Proc. Natl. Acad. Sci, vol.103, pp.19771-19776, 2006.

M. Théry, V. Racine, A. Pépin, M. Piel, Y. Chen et al., The extracellular matrix guides the orientation of the cell division axis, Nat. Cell Biol, vol.7, pp.947-953, 2005.

C. Formosa, M. Grare, E. Jauvert, A. Coutable, M. Mourer et al., Nanoscale analysis of the effects of antibiotics and CX1 on a Pseudomonas aeruginosa multidrugresistant strain, J.B
URL : https://hal.archives-ouvertes.fr/hal-01650390

C. Formosa, M. Herold, C. Vidaillac, R. E. Duval, and E. Dague, Unravelling of a mechanism of resistance to colistin in Klebsiella pneumoniae using atomic force microscopy, J. Antimicrob. Chemother, vol.70, pp.2261-2270, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01553126

T. A. Camesano, M. J. Natan, and B. E. Logan, Observation of changes in bacterial cell morphology using tapping mode atomic force microscopy, Langmuir, vol.16, pp.4563-4572, 2000.

R. J. Emerson and T. A. Camesano, Nanoscale investigation of pathogenic microbial adhesion to a biomaterial, Appl. Environ. Microbiol, vol.70, pp.6012-6022, 2004.

A. Cerf, J. Cau, and C. Vieu, Controlled assembly of bacteria on chemical patterns using soft lithography, Colloids Surf. B Biointerfaces, vol.65, pp.285-291, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02061195

L. Ressier, B. Viallet, A. Beduer, D. Fabie, L. Fabié et al., Combining convective/capillary deposition and AFM oxidation lithography for close-packed directed assembly of colloids, Langmuir, vol.24, pp.13254-13257, 2008.

A. Cerf, J. Cau, C. Vieu, and E. Dague, Nanomechanical properties of dead or alive single-patterned bacteria, Langmuir, vol.25, pp.5731-5736, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02061192

E. Jauvert, E. Palleau, E. Dague, and L. Ressier, Directed Assembly of Living Pseudomonas aeruginosa Bacteria on PEI Patterns Generated by Nanoxerography for Statistical AFM Bioexperiments, ACS Appl. Mater. Interfaces, vol.6, pp.21230-21236, 2014.

A. Kumar, H. A. Biebuyck, and G. M. Whitesides, Patterning Self-Assembled Monolayers: Applications in Materials Science, Langmuir, vol.10, pp.1498-1511, 1994.

C. Thibault, C. Severac, E. Trevisiol, and C. Vieu, Microtransfer molding of hydrophobic dendrimer, Microelectron. Eng, vol.83, pp.1513-1516, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01767488

F. Hua, Y. Sun, A. Gaur, M. A. Meitl, L. Bilhaut et al., Polymer Imprint Lithography with Molecular-Scale Resolution, Nano. Lett, vol.4, pp.2467-2471, 2004.

R. S. Kane, S. Takayama, E. Ostuni, D. E. Ingber, and G. M. Whitesides, Patterning proteins and cells using soft lithography, Biomaterials, vol.20, pp.2363-2376, 1999.

M. Mrksich and G. M. Whitesides, Using self-assembled monolayers to understand the interactions of man-made surfaces with proteins and cells, Annu. Rev. Biophys. Biomol. Struct, vol.25, p.347, 1996.

S. Zhang, L. Yan, M. Altman, M. Lässle, H. Nugent et al., Biological surface engineering: A simple system for cell pattern formation, Biomaterials, vol.20, pp.1213-1220, 1999.

S. A. Ruiz and C. S. Chen, Microcontact printing: A tool to pattern, Soft Matter, vol.3, pp.168-177, 2007.

M. Long, M. Sato, C. T. Lim, J. Wu, T. Adachi et al., Advances in Experiments and Modeling in Microand Nano-Biomechanics: A Mini Review. Cell. Mol. Bioeng, vol.4, pp.327-339, 2011.

J. Foncy, J. Cau, C. Bartual-murgui, J. M. François, E. Trévisiol et al., Comparison of polyurethane and epoxy resist master mold for nanoscale soft lithography, Microelectron. Eng, vol.110, pp.183-187, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01848847

L. Wong, J. D. Pegan, B. Gabela-zuniga, M. Khine, and K. E. Mccloskey, Leaf-inspired microcontact printing vascular patterns, vol.9, 2017.

L. Malaquin, T. Kraus, H. Schmid, E. Delamarche, and H. Wolf, Controlled Particle Placement through Convective and Capillary Assembly, Langmuir, vol.23, pp.11513-11521, 2007.

J. Fredonnet, J. Foncy, S. Lamarre, J. Cau, E. Trévisiol et al., Dynamic PDMS inking for DNA patterning by soft lithography, Microelectron. Eng, vol.111, pp.379-383, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01848833

H. Cayron, B. Berteloite, C. Vieu, V. Paveau, J. Cau et al., Controlled deposition and multi-layer architecturing of single biomolecules using automated directed capillary assembly and nano-contact printing processes, Microelectron. Eng, vol.135, pp.1-6, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01213795

F. Delapierre, G. Mottet, V. Taniga, J. Boisselier, J. Viovy et al., High throughput micropatterning of interspersed cell arrays using capillary assembly, vol.9, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01852026

A. Lagraulet, J. Foncy, B. Berteloite, A. Esteve, M. Blatche et al., InnoStamp 40 TM and InnoScan 1100AL TM : A complete automated platform for microstructured cell arrays, Nat. Methods, vol.12, 2015.

J. D. Mcnulty, T. Klann, J. Sha, M. Salick, G. T. Knight et al., High-precision robotic microcontact printing (R-µCP) utilizing a vision guided selectively compliant articulated robotic arm, Lab Chip, vol.14, 1923.

G. T. Knight, T. Klann, J. D. Mcnulty, and R. S. Ashton, Fabricating Complex Culture Substrates Using Robotic Microcontact Printing (R-µCP) and Sequential Nucleophilic Substitution, J. Vis. Exp. JoVE, 2014.

S. G. Ricoult, A. Sanati-nezhad, M. Knapp-mohammady, T. E. Kennedy, and D. Juncker, Humidified Microcontact Printing of Proteins: Universal Patterning of Proteins on Both Low and High Energy Surfaces, Langmuir, vol.30, pp.12002-12010, 2014.

S. R. Polio and M. L. Smith, Patterned Hydrogels for Simplified Measurement of Cell Traction Forces, Methods Cell Biol, vol.121, pp.17-31, 2014.

S. R. Vedula, H. Hirata, M. H. Nai, A. Brugués, Y. Toyama et al., Epithelial bridges maintain tissue integrity during collective cell migration, Nat. Mater, vol.13, pp.87-96, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00951190

K. El-kirat, I. Burton, V. Dupres, and Y. F. Dufrene, Sample preparation procedures for biological atomic force microscopy, J. Microsc, vol.218, pp.199-207, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00017269

L. Kailas, E. C. Ratcliffe, E. J. Hayhurst, M. G. Walker, S. J. Foster et al., Immobilizing live bacteria for AFM imaging of cellular processes, Ultramicroscopy, vol.109, pp.775-780, 2009.

E. Dague, E. Jauvert, L. Laplatine, B. Viallet, C. Thibault et al., Assembly of live micro-organisms on microstructured PDMS stamps by convective/capillary deposition for AFM bio-experiments, Nanotechnology, vol.22, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01767584

S. W. Rhee, A. M. Taylor, C. H. Tu, D. H. Cribbs, C. W. Cotman et al., Patterned cell culture inside microfluidic devices, Lab Chip, vol.5, pp.102-107, 2005.

Y. Torisawa, B. Mosadegh, G. D. Luker, M. Morell, K. S. O'shea et al., Microfluidic hydrodynamic cellular patterning for systematic formation of co-culture spheroids, Integr. Biol, vol.1, pp.649-654, 2009.

C. Tu, B. Huang, J. Zhou, Y. Liang, J. Tian et al., A Microfluidic Chip for Cell Patterning Utilizing Paired Microwells and Protein Patterns, vol.8, 2017.

, Micromachines 2017, vol.8

A. Azioune, N. Carpi, Q. Tseng, M. Théry, and M. Piel, Chapter 8-Protein Micropatterns: A Direct Printing Protocol Using Deep UVs, In Methods in Cell Biology

L. Cassimeris, P. Tran, and . Eds, , vol.97, pp.133-146, 2010.

N. Carpi, M. Piel, A. Azioune, D. Cuvelier, and J. Fink, Micropatterning on silicon elastomer (PDMS) with deep UVs, Protoc. Exch, 2011.

N. Carpi, M. Piel, A. Azioune, and . Fink, J. Micropatterning on glass with deep UV. Protoc. Exch, 2011.

A. , , p.20, 2017.

F. F. Hulshof, Y. Zhao, A. Vasilevich, N. R. Beijer, M. De-boer et al., High-throughput nanotopographical cell instruction, Acta Biomater, vol.62, pp.188-198, 2017.

M. Li, L. Liu, N. Xi, and Y. Wang, Biological Applications of a Nanomanipulator Based on AFM: In situ visualization and quantification of cellular behaviors at the single-molecule level, IEEE Nanotechnol. Mag, vol.9, pp.25-35, 2015.

H. Fortier, F. Variola, C. Wang, and S. Zou, AFM force indentation analysis on leukemia cells, Anal. Methods, vol.8, pp.4421-4431, 2016.

E. Minelli, G. Ciasca, T. E. Sassun, M. Antonelli, V. Palmieri et al., A fully-automated neural network analysis of AFM force-distance curves for cancer tissue diagnosis, Appl. Phys. Lett, vol.111, 2017.

, This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, © 2017 by the authors. Licensee MDPI

M. C. Piontek and W. H. Roos, Atomic Force Microscopy: An Introduction, Single Molecule Analysis: Methods and Protocols

, , pp.243-258, 2018.

C. Formosa and E. Dague, Imaging Living Yeast Cells and Quantifying Their Biophysical Properties by Atomic Force Microscopy, Advanced Microscopy in Mycology

T. E. Dahms and K. J. Czymmek, Fungal Biology, pp.125-141, 2015.

L. A. Bottomley, E. D. Gadsby, and M. A. Poggi, MICROSCOPY TECHNIQUES | Atomic Force and Scanning Tunneling Microscopy, Encyclopedia of Analytical Science

P. Worsfold, A. Townshend, and C. Poole, , pp.143-151, 2005.

A. J. Malkin, T. A. Land, Y. G. Kuznetsov, A. Mcpherson, and J. J. Deyoreo, Investigation of Virus Crystal Growth Mechanisms by In Situ Atomic Force Microscopy, Phys. Rev. Lett, issue.14, pp.2778-2781, 1995.

M. Rief, M. Gautel, F. Oesterhelt, J. M. Fernandez, and H. E. Gaub, Reversible Unfolding of Individual Titin Immunoglobulin Domains by AFM, Science, vol.276, issue.5315, pp.1109-1112, 1997.

N. J. Tao, S. M. Lindsay, and S. Lees, Measuring the Microelastic Properties of Biological Material, Biophys. J, vol.63, issue.4, pp.1165-1169, 1992.

A. Meister, M. Gabi, P. Behr, P. Studer, J. Vörös et al., Combining Atomic Force Microscopy and Nanofluidics in a Universal Liquid Delivery System for Single Cell Applications and Beyond, Nano Lett, vol.9, issue.6, pp.2501-2507, 2009.

T. Ando, N. Kodera, E. Takai, D. Maruyama, K. Saito et al., A High-Speed Atomic Force Microscope for Studying Biological Macromolecules, Proc. Natl. Acad. Sci, vol.98, pp.12468-12472, 2001.

A. Syahir, K. Usui, K. Tomizaki, K. Kajikawa, and H. Mihara, Label and Label-Free Detection Techniques for Protein Microarrays, vol.4, pp.228-244, 2015.

A. Touhami, B. Nysten, and Y. F. Dufrêne, Nanoscale Mapping of the Elasticity of Microbial Cells by Atomic Force Microscopy, Langmuir, vol.19, issue.11, pp.4539-4543, 2003.

D. Alsteens, V. Dupres, K. M. Evoy, L. Wildling, H. J. Gruber et al., Cell Wall Elasticity and Polysaccharide Properties of Living Yeast Cells, as Probed by AFM, vol.19, p.384005, 2008.

F. Pillet, S. Lemonier, M. Schiavone, C. Formosa, H. Martin-yken et al., Uncovering by Atomic Force Microscopy of an Original Circular Structure at the Yeast Cell Surface in Response to Heat Shock, BMC Biol, vol.12, issue.1, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02639992

M. Schiavone, N. Sieczkowski, M. Castex, E. Dague, and J. Marie-françois, Effects of the Strain Background and Autolysis Process on the Composition and Biophysical Properties of the Cell Wall from Two Different Industrial Yeasts, FEMS Yeast Res, issue.2, p.15, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01553141

C. Formosa, M. Schiavone, A. Boisrame, M. L. Richard, R. E. Duval et al., Multiparametric Imaging of Adhesive Nanodomains at the Surface of Candida Albicans by Atomic Force Microscopy, Nanomedicine Nanotechnol. Biol. Med, vol.11, issue.1, pp.57-65, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01553144

H. Martin-yken, T. Bedekovic, A. C. Brand, M. L. Richard, S. Znaidi et al., A Conserved Fungal Hub Protein Involved in Adhesion and Drug Resistance in the Human Pathogen Candida Albicans, Cell Surf, vol.4, pp.10-19, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02091662

,

P. C. Braga and D. Ricci, Differences in the Susceptibility of Streptococcus Pyogenes to Rokitamycin and Erythromycin A Revealed by Morphostructural Atomic Force Microscopy

, J. Antimicrob. Chemother, vol.50, issue.4, pp.457-460, 2002.

C. Formosa, M. Grare, R. E. Duval, and E. Dague, Nanoscale Effects of Antibiotics on P. Aeruginosa. Nanomedicine Nanotechnol. Biol. Med, vol.2012, issue.1, pp.12-16

M. Lekka, P. Laidler, D. Gil, J. Lekki, Z. Stachura et al., Elasticity of Normal and Cancerous Human Bladder Cells Studied by Scanning Force Microscopy, Eur. Biophys. J, vol.28, issue.4, pp.312-316, 1999.

S. E. Cross, Y. Jin, J. Rao, and J. Gimzewski, Nanomechanical Analysis of Cells from Cancer Patients, Nat. Nanotechnol, vol.2, issue.12, pp.780-783, 2007.

,

R. Omidvar, M. Tafazzoli-shadpour, M. A. Shokrgozar, and M. Rostami, Atomic Force Microscope-Based Single Cell Force Spectroscopy of Breast Cancer Cell Lines: An Approach for Evaluating Cellular Invasion, J. Biomech, vol.47, issue.13, pp.3373-3379, 2014.

L. Bastatas, D. Martinez-marin, J. Matthews, J. Hashem, Y. J. Lee et al., AFM Nano-Mechanics and Calcium Dynamics of Prostate Cancer Cells with Distinct Metastatic Potential, Biochim. Biophys. Acta BBA -Gen. Subj, vol.2012, issue.7, pp.1111-1120

G. Smolyakov, B. Thiebot, C. Campillo, S. Labdi, C. Severac et al., Adhesion, and Tether Extrusion on Breast Cancer Cells Provide a Signature of Their Invasive Potential, ACS Appl. Mater. Interfaces, vol.8, issue.41, pp.27426-27431, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01552762

H. J. Sanyour, N. Li, A. P. Rickel, J. D. Childs, C. N. Kinser et al., Membrane Cholesterol and Substrate Stiffness Co-Ordinate to Induce the Remodelling of the Cytoskeleton and the Alteration in the Biomechanics of Vascular Smooth Muscle Cells, Cardiovasc. Res, vol.115, issue.8, pp.1369-1380, 2019.

M. Lekka, M. Fornal, G. Pyka-fo?ciak, K. Lebed, B. Wizner et al., Erythrocyte Stiffness Probed Using Atomic Force Microscope, Biorheology, vol.42, issue.4, pp.307-317, 2005.

I. Duli?ska, M. Targosz, W. Strojny, M. Lekka, P. Czuba et al., Stiffness of Normal and Pathological Erythrocytes Studied by Means of Atomic Force 79 Microscopy, J. Biochem. Biophys. Methods, vol.66, issue.1, pp.1-11, 2006.

,

J. C. Benech, N. Benech, A. I. Zambrana, I. Rauschert, V. Bervejillo et al., Diabetes Increases Stiffness of Live Cardiomyocytes Measured by Atomic Force Microscopy Nanoindentation, Am. J. Physiol.-Cell Physiol, vol.307, issue.10, pp.910-919, 2014.

E. Dague, G. Genet, V. Lachaize, C. Guilbeau-frugier, J. Fauconnier et al., Atomic Force and Electron Microscopic-Based Study of Sarcolemmal Surface of Living Cardiomyocytes Unveils Unexpected Mitochondrial Shift in Heart Failure, J. Mol. Cell. Cardiol, vol.74, pp.162-172, 2014.
URL : https://hal.archives-ouvertes.fr/inserm-01016102

A. Martinez-rivas, G. K. González-quijano, S. Proa-coronado, C. Séverac, and E. Dague, Methods of Micropatterning and Manipulation of Cells for Biomedical Applications, vol.8, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01907683

B. Städler, D. Falconnet, I. Pfeiffer, F. Höök, and J. Vörös, Micropatterning of DNA-Tagged Vesicles, Langmuir, vol.20, issue.26, pp.11348-11354, 2004.

R. Estevam-alves, P. H. Ferreira, A. C. Coatrini, O. N. Oliveira, C. R. Fontana et al., Femtosecond Laser Patterning of the Biopolymer Chitosan for Biofilm Formation, Int. J. Mol. Sci, vol.2016, issue.8, p.1243

G. Huang, Y. Mei, D. J. Thurmer, E. Coric, and O. G. Schmidt, Rolled-up Transparent Microtubes as Two-Dimensionally Confined Culture Scaffolds of Individual Yeast Cells, Lab. Chip, vol.9, issue.2, pp.263-268, 2009.

C. Credi, C. De-marco, E. Molena, M. Pla-roca, J. Samitier-martí et al., Heparin Micropatterning onto Fouling-Release Perfluoropolyether-Based Polymers via Photobiotin Activation, Colloids Surf. B Biointerfaces, vol.146, pp.250-259, 2016.

P. Y. Chiou, A. T. Ohta, and M. C. Wu, Massively Parallel Manipulation of Single Cells and Microparticles Using Optical Images, Nature, vol.436, issue.7049, pp.370-372, 2005.

P. Jing, J. Wu, G. W. Liu, E. G. Keeler, S. H. Pun et al., Photonic Crystal Optical Tweezers with High Efficiency for Live Biological Samples and Viability Characterization, Sci. Rep, vol.6, issue.1, pp.1-7, 2016.

A. Yusof, H. Keegan, C. D. Spillane, O. M. Sheils, C. M. Martin et al., Inkjet-like Printing of Single-Cells, Lab. Chip, vol.11, issue.14, pp.2447-2454, 2011.

Q. Zheng, J. Lu, H. Chen, L. Huang, J. Cai et al., Application of Inkjet Printing Technique for Biological Material Delivery and Antimicrobial Assays, Anal. Biochem, vol.410, issue.2, pp.171-176, 2011.

X. Ding, S. S. Lin, B. Kiraly, H. Yue, S. Li et al., On-Chip Manipulation of Single Microparticles, Cells, and Organisms Using Surface Acoustic Waves, Proc. Natl. Acad. Sci, vol.109, pp.11105-11109, 2012.

S. M. Naseer, A. Manbachi, M. Samandari, P. Walch, Y. Gao et al., Surface Acoustic Waves Induced Micropatterning of Cells in Gelatin Methacryloyl (GelMA) Hydrogels. Biofabrication, vol.9, issue.1, p.15020, 2017.

J. Pivetal, D. Royet, G. Ciuta, M. Frenea-robin, N. Haddour et al., Micro-Magnet Arrays for Specific Single Bacterial Cell Positioning, J. Magn. Magn. Mater, vol.380, pp.72-77, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01113985

G. R. Souza, H. Tseng, J. A. Gage, A. Mani, P. Desai et al., Magnetically Bioprinted Human Myometrial 3D Cell Rings as A Model for Uterine Contractility, Int. J. Mol. Sci, vol.2017, issue.4

M. Théry, V. Racine, M. Piel, A. Pépin, A. Dimitrov et al., Anisotropy of Cell Adhesive Microenvironment Governs Cell Internal Organization and Orientation of Polarity, Proc. Natl. Acad. Sci, vol.103, pp.19771-19776, 2006.

A. Cerf, J. Cau, C. Vieu, and E. Dague, Nanomechanical Properties of Dead or Alive Single-Patterned Bacteria, Langmuir, vol.25, issue.10, pp.5731-5736, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02061192

L. Ressier, B. Viallet, A. Beduer, D. Fabre, L. Fabie et al., Combining Convective/Capillary Deposition and AFM Oxidation Lithography for Close-Packed Directed Assembly of Colloids, Langmuir, vol.24, issue.23, pp.13254-13257, 2008.

,

L. Malaquin, T. Kraus, H. Schmid, E. Delamarche, and H. Wolf, Controlled Particle Placement through Convective and Capillary Assembly, Langmuir, vol.23, issue.23, pp.11513-11521, 2007.

C. Formosa, F. Pillet, M. Schiavone, R. E. Duval, L. Ressier et al., Generation of Living Cell Arrays for Atomic Force Microscopy Studies, Nat. Protoc, vol.10, issue.1, pp.199-204, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01495201

E. Dague, E. Jauvert, L. Laplatine, B. Viallet, C. Thibault et al., Assembly of Live Micro-Organisms on Microstructured PDMS Stamps by Convective/Capillary Deposition for AFM Bio-Experiments, Nanotechnology, vol.22, issue.39, p.395102, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01767584

F. F. Hulshof, Y. Zhao, A. Vasilevich, N. R. Beijer, M. De-boer et al., High-Throughput Nanotopographical Cell Instruction, Acta Biomater, vol.62, pp.188-198, 2017.

,

, PRIMO: Micropatterning, Microfabrication and Hydrogel Structuration. alvéole

Z. Wang, L. Liu, Y. Wang, N. Xi, Z. Dong et al., Automated System for Measuring Cellular Mechanical Properties, J. Lab. Autom, vol.2012, issue.6, pp.443-448

R. Roy, W. Chen, L. Cong, L. A. Goodell, D. J. Foran et al., A Semi-Automated Positioning System for Contact-Mode Atomic Force Microscopy (AFM)

. Autom, . Sci, and . Eng, , vol.10, pp.462-465, 2013.

M. Favre, J. Polesel-maris, T. Overstolz, P. Niedermann, S. Dasen et al., Parallel AFM Imaging and Force Spectroscopy Using Two-Dimensional Probe Arrays for Applications in Cell Biology, J. Mol. Recognit, vol.24, issue.3, pp.446-452, 2011.

H. Sadeghian, R. Herfst, B. Dekker, J. Winters, T. Bijnagte et al., High-Throughput Atomic Force Microscopes Operating in Parallel, Rev. Sci. Instrum, vol.2017, issue.3, p.33703

A. Dujardin, P. D. Wolf, F. Lafont, and V. Dupres, Automated Multi-Sample Acquisition and Analysis Using Atomic Force Microscopy for Biomedical Applications, PLOS ONE, vol.2019, issue.3
URL : https://hal.archives-ouvertes.fr/inserm-02229466

M. J. Madou, Fundamentals of Microfabrication: The Science of Miniaturization, ) Encyclopedia of Nanotechnology | SpringerLink, vol.29, 2002.

C. Formosa, M. Schiavone, H. Martin-yken, J. M. François, R. E. Duval et al., Nanoscale Effects of Caspofungin against Two Yeast Species, Saccharomyces Cerevisiae and Candida Albicans, Antimicrob. Agents Chemother, vol.2013, issue.8, pp.3498-3506
URL : https://hal.archives-ouvertes.fr/hal-02937573

B. G. Prevo, O. D. Velev, and . Controlled, Rapid Deposition of Structured Coatings from Microand Nanoparticle Suspensions, Langmuir, vol.20, issue.6, pp.2099-2107, 2004.

,

L. Malaquin, T. Kraus, H. Schmid, E. Delamarche, and H. Wolf, Controlled Particle Placement through Convective and Capillary Assembly, Langmuir, vol.23, issue.23, pp.11513-11521, 2007.

Y. Yin, Y. Lu, B. Gates, and Y. Xia, Template-Assisted Self-Assembly: A Practical Route to Complex Aggregates of Monodispersed Colloids with Well-Defined Sizes, Shapes, and Structures, J. Am. Chem. Soc, vol.123, issue.36, pp.8718-8729, 2001.

C. Formosa and E. Dague, Imaging Living Yeast Cells and Quantifying Their Biophysical Properties by Atomic Force Microscopy, Advanced Microscopy in Mycology

T. E. Dahms and K. J. Czymmek, Fungal Biology, pp.125-141, 2015.

S. Proa-coronado, C. Séverac, A. Martinez-rivas, and E. Dague, Beyond the Paradigm of Nanomechanical Measurements on Cells Using AFM: An Automated Methodology to Rapidly Analyse Thousands of Cells, Nanoscale Horiz, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02321293

C. Formosa, F. Pillet, M. Schiavone, R. E. Duval, L. Ressier et al., Generation of Living Cell Arrays for Atomic Force Microscopy Studies, Nat. Protoc, vol.10, issue.1, pp.199-204, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01495201

A. Lagraulet, J. Foncy, B. Berteloite, A. Esteve, M. Blatche et al., InnoStamp 40 TM and InnoScan 1100AL TM : A Complete Automated Platform for Microstructured Cell Arrays, Nat. Methods, vol.12, pp.894-894, 2015.

,

M. ;. Mansfield and . O'sullivan, C. Understanding Physics

K. L. Johnson, One Hundred Years of Hertz Contact, Proc. Inst. Mech. Eng, vol.196, issue.1, pp.363-378, 1982.

I. N. Sneddon, The Relation between Load and Penetration in the Axisymmetric Boussinesq Problem for a Punch of Arbitrary Profile, Int. J. Eng. Sci, vol.1965, issue.1, pp.47-57

D. Freedman and P. Diaconis, On the Histogram as a Density Estimator:L2 Theory. Z. Für Wahrscheinlichkeitstheorie Verwandte Geb, vol.57, pp.453-476, 1981.

,

D. W. Scott, Multivariate Density Estimation: Theory, Practice, and Visualization, 1992.

J. A. Hartigan and M. A. Wong, Algorithm AS 136: A K-Means Clustering Algorithm, J. R. Stat. Soc. Ser. C Appl. Stat, vol.28, issue.1, pp.100-108, 1979.

. R-core-team, R: A Language and Enviroment for Statistical Computing; R Foundation for Statistical Computing, 2018.

C. Formosa, F. Pillet, M. Schiavone, R. E. Duval, L. Ressier et al., Generation of Living Cell Arrays for Atomic Force Microscopy Studies, Nat. Protoc, vol.10, issue.1, pp.199-204, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01495201

G. Hwang, G. Marsh, L. Gao, R. Waugh, and H. Koo, Binding Force Dynamics of Streptococcus Mutans-Glucosyltransferase B to Candida Albicans, J. Dent. Res, vol.94, issue.9, pp.1310-1317, 2015.

G. Hwang, Y. Liu, D. Kim, Y. Li, D. J. Krysan et al., Candida Albicans Mannans Mediate Streptococcus Mutans Exoenzyme GtfB Binding to Modulate Cross-Kingdom Biofilm Development in Vivo, PLOS Pathog, vol.13, issue.6, 2017.

S. Ma, W. Ge, Y. Yan, X. Huang, L. Ma et al., Effects of Streptococcus sanguinis Bacteriocin on Deformation, Adhesion Ability, and Young's Modulus of Candida albicans, 2019.

C. Formosa-dague, R. E. Duval, and E. Dague, Cell Biology of Microbes and Pharmacology of Antimicrobial Drugs Explored by Atomic Force Microscopy. Semin. Cell Dev. Biol, vol.73, pp.165-176, 2018.

C. Formosa, M. Schiavone, H. Martin-yken, J. M. François, R. E. Duval et al., Nanoscale Effects of Caspofungin against Two Yeast Species, Saccharomyces Cerevisiae and Candida Albicans, Antimicrob. Agents Chemother, vol.2013, issue.8, pp.3498-3506
URL : https://hal.archives-ouvertes.fr/hal-02937573

S. El-kirat-chatel, A. Beaussart, D. Alsteens, D. N. Jackson, P. N. Lipke et al., Nanoscale Analysis of Caspofungin-Induced Cell Surface Remodelling in Candida Albicans, Nanoscale, vol.2013, issue.3, pp.1105-1115

D. C. Poulain and . Albicans, Plasticity and Pathogenesis, Crit. Rev. Microbiol, vol.41, issue.2, pp.208-217, 2015.

G. Binnig, H. Rohrer, C. Gerber, and E. Weibel, Surface Studies by Scanning Tunneling Microscopy, Phys. Rev. Lett, vol.1982, issue.1, pp.57-61

T. Monrousseau, L. Travé-massuyès, and M. Le-lann, Processing Measure Uncertainty into Fuzzy Classifier, 26th International Workshop on Principles of Diagnosis
URL : https://hal.archives-ouvertes.fr/hal-01274212

F. Paris, , 2015.

Z. Fang, C. Jiang, Y. Feng, R. Chen, X. Lin et al., Effects of G6PD Activity Inhibition on the Viability, ROS Generation and Mechanical Properties of Cervical Cancer Cells, Biochim. Biophys. Acta BBA -Mol. Cell Res, issue.9, pp.2245-2254, 2016.

H. G. Abdelhady, H. A. Salam, E. M. Niazy, A. Mueller, M. J. Quast et al., Spatiotemporal PFQNM Visualization of the Effect of Suicide Dendriplexes on Dividing HeLa Cells, vol.12, pp.2365-2371, 2016.

I. Dulínska-molak, H. Mao, N. Kawazoe, and G. Chen, Variation of Mechanical Property of Single-Walled Carbon Nanotubes-Treated Cells Explored by Atomic Force Microscopy, 2019.

,

T. M. Cytoochips and . Starter, , 2019.

P. J. Albert and U. S. Schwarz, Dynamics of Cell Shape and Forces on Micropatterned Substrates Predicted by a Cellular Potts Model, Biophys. J, vol.106, issue.11, pp.2340-2352, 2014.

N. I. Petridou and P. A. Skourides, FAK Transduces Extracellular Forces That Orient the Mitotic Spindle and Control Tissue Morphogenesis, Nat. Commun, vol.2014, issue.1, pp.1-16

A. Lagraulet, J. Foncy, B. Berteloite, A. Esteve, M. Blatche et al., InnoStamp 40 TM and InnoScan 1100AL TM : A Complete Automated Platform for Microstructured Cell Arrays, Nat. Methods, vol.12, pp.894-894, 2015.

,

N. A. Gow, F. L. Van-de-veerdonk, A. J. Brown, and M. G. Netea, Candida Albicans Morphogenesis and Host Defence: Discriminating Invasion from Colonization, Nat. Rev. Microbiol, vol.10, issue.2, pp.112-122, 2011.

E. Dague, E. Jauvert, L. Laplatine, B. Viallet, C. Thibault et al., Assembly of Live Micro-Organisms on Microstructured PDMS Stamps by Convective/Capillary Deposition for AFM Bio-Experiments, Nanotechnology, vol.22, issue.39, p.395102, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01767584

J. J. Harrison, R. J. Turner, and H. Ceri, A Subpopulation of Candida Albicans and Candida Tropicalis Biofilm Cells Are Highly Tolerant to Chelating Agents, FEMS Microbiol. Lett, issue.2, pp.172-181, 2007.

P. D. Khot, P. A. Suci, R. L. Miller, R. D. Nelson, and B. J. Tyler, A Small Subpopulation of Blastospores in Candida Albicans Biofilms Exhibit Resistance to Amphotericin B Associated with Differential Regulation of Ergosterol and ?-1,6-Glucan Pathway Genes, Antimicrob. Agents Chemother, vol.50, issue.11, pp.3708-3716, 2006.

M. Schiavone, S. Déjean, N. Sieczkowski, M. Castex, E. Dague et al., Integration of Biochemical, Biophysical and Transcriptomics Data for Investigating the Structural and Nanomechanical Properties of the, Yeast Cell Wall. Front. Microbiol, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01698344

A. Rosenberg, I. V. Ene, M. Bibi, S. Zakin, E. S. Segal et al., Antifungal Tolerance Is a Subpopulation Effect Distinct from Resistance and Is Associated with Persistent Candidemia, Nat. Commun, vol.9, issue.1, p.2470, 2018.

P. W. Groot and . De,

O. Bader, A. D. Boer, M. Weig, and N. Chauhan, Adhesins in Human Fungal Pathogens: Glue with Plenty of Stick, Eukaryot. Cell, vol.12, issue.4, pp.470-481, 2013.

C. Formosa, M. Schiavone, A. Boisrame, M. L. Richard, R. E. Duval et al., Multiparametric Imaging of Adhesive Nanodomains at the Surface of Candida Albicans by Atomic Force Microscopy, Nanomedicine Nanotechnol. Biol. Med, vol.11, issue.1, pp.57-65, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01553144

P. Sajeesh, A. Raj, M. Doble, and A. K. Sen, Characterization and Sorting of Cells Based on Stiffness Contrast in a Microfluidic Channel, RSC Adv, vol.2016, issue.78, pp.74704-74714

K. B. Tománková, P. Kolar, J. Malohlava, and H. Kolá?ová, Mechanical Characterisation of HeLa Cells Using Atomic Force Microscopy

C. Formosa, F. Pillet, M. Schiavone, R. E. Duval, L. Ressier et al., Generation of Living Cell Arrays for Atomic Force Microscopy Studies, Nat. Protoc, vol.10, issue.1, pp.199-204, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01495201

L. Hedjazi, J. Aguilar-martin, and M. Le-lann, Similarity-Margin Based Feature Selection for Symbolic Interval Data, Pattern Recognit. Lett, vol.32, issue.4, pp.578-585, 2011.

L. Hedjazi, J. Aguilar-martin, M. Le-lann, and T. Kempowsky-hamon, Membership-Margin Based Feature Selection for Mixed Type and High-Dimensional Data: Theory and Applications, Inf. Sci, vol.322, pp.174-196, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01998674

T. Kempowsky-hamon, C. Valle, M. Lacroix-triki, L. Hedjazi, L. Trouilh et al., Fuzzy Logic Selection as a New Publications in interantional Peer reviewed journals 1, JoVe, 2020.

C. Séverac, S. Proa-coronado, C. Formosa-dague, A. Martinez-rivas, and E. Dague,

, Nanoscale Horizons, 2020.

S. Proa-coronado, C. Séverac, A. Martínez-rivas, and E. Dague,

, Micromachines, vol.8, p.347, 2017.

A. Martinez-rivas, K. González-quijano, S. Proa-coronado, and C. Séverac,

A. Rivas, E. Dague, S. Coronado, C. Séverac, and G. K. González,

R. Número-de, , vol.1, pp.3-2017

E. Dague, S. Coronado, C. Séverac, and A. Martinez-rivas-automatip, Automatización de mediciones biofísicas en células por medio del microscopio de fuerza atómica

, BiophysAdh: International symposium on biophysics of microbial adhesion, vol.1, pp.10-11, 2018.

S. Proa-coronado, C. Séverac, E. Dague, and A. Martinez-rivas,

, ICTNN2018: International congress on transdisciplinary nanoscience & nanotechnology. 28th-31th, 2018.

C. Proa-coronado, E. Severac, A. Dague, and . Martinez-rivas, IMRC 2017: XXVI International Materials Research Congress, 2017.

. Nanobio-tecnopoli, NanoBio meeting, 2018.

S. Proa-coronado, C. Severac, E. Dague, and A. Martinez-rivas,

, MNE 2018: Micro & Nano Engineering, pp.24-27, 2018.

S. Proa-coronado, C. Séverac, A. Martínez-rivas, and E. Dague,

, Linz winter workshop: XXI Annual Linz Winter Workshop. 1-4, 2019.

S. Proa-coronado, C. Séverac, A. Martínez-rivas, and E. Dague,

, IMRC 2019: XXVIII International Materials Research Congress, 2019.

A. Bruker, . User, A. Proa-coronado, E. Martínez-rivas, C. Dague et al., AFM automation on living cells 2. BIOSURF 2019: École thématique CNRS «BIOSURF, pp.27-28, 2018.

S. Proa-coronado, C. Séverac, A. Martínez-rivas, and E. Dague,

. Instituto and . Nacional,

L. A. Edificio-de, A. V. Dirección-general, . Luis-enrique, . Erro-s/n-07738, . Mexico et al.,

, += extraDistance print 'FastLength modified' + str

+. Slowlength, / 2)) > 50e-6: extraDistance = ((P[1] + SlowLength / 2) -50e-6), pp.1-6

, += extraDistance print 'SlowLength modified' the tip Snapshooter.saveOpticalSnapshot(path+"initialP-"+ str(dateTemp) + ".png") ForceSpectroscopy.setGridPattern(FastLength, SlowLength, XGridCenter, YGridCenter, NumFastPoints, NumSlowPoints, a) #ForceSpectroscopy.setGridPattern(FastLength, SlowLength, XGridCenter, YGridCenter, NumFastPoints, NumSlowPoints, a) Scanner.approach() # Iterating through the grid for h in range(NumFastPoints * NumSlowPoints): Scanner.retractPiezo() ForceSpectroscopy.moveToForcePositionIndex(h) Scanner.approachPiezo(

+. Temp and . Scanner, ): tempX += PH

, y) logFile = open(fileName, "a") logFile.write('Motor stage current coordinate '+ str(g)+': '+str(MSCoord[g].x)+str(MSCoord[g].y) + "\n") logFile.close() print 'Motor stage current coordinate '+ str(g)+': '+str, 0: #Engaging MotorStage MotorizedStage.engage() #Moving the MotorStage to a particular coordinate MotorizedStage.moveToAbsolutePosition

, for i in range(nFP*nSP): WellPositions.append

, # Calculating Well positions if option == 0: for f in range(1, nFP): in range(0, len(WellPositions) -nFP): if i < 1: i = (nFP*

, # Print the WellGrid current position logFile = open(fileName, "a") logFile.write('Current Well: '+ str(index) + "\n") logFile.close() print 'Current position on Wellgrid

, # set the directory where the force scans should be stored HAVE FUN date = time.asctime() ForceSpectroscopy.setOutputDirectory(pathR+"/WellGrid" +str(index) + '--' + str

. Fastlength, . Slowlength, . Xgridcenter, and N. Ygridcenter, NumSlowPoints, angle) Scanner.approachPiezo() #Iterating through the measurement grid ForceSpectroscopy.startScansPerPosition(1) Scanner.retractPiezo() except: print 'This well has some points outside the scanning area\nProceeding to the next one

, + str(ele.y) len(MSCoord): #initialMStime=time.time() #Retract the scanner to avoid damages #Scanner.retract() ForceSpectroscopy.setPosition

, 0: #Engaging MotorStage MotorizedStage.engage() #Moving the MotorStage to a particular coordinate MotorizedStage.moveToAbsolutePosition

, +': '+str

, y) + "\n") #logFile.close() MotorizedStage.disengage() print 'Motor stage current coordinate '+ str(g)+': '+str(MotorizedStage.getPosition(

, getY()) #MotorizedStage.disengage() #calculatePoints(Ws,angle,fileName, fineCoord) Scanner.approachPiezo() if choice == 0: ForceMapping.activateGUIMode() ForceMapping.Autosave.on() ForceMapping.setOutputDirectory(path+"/Cell

. Forcemapping, , pp.50-56

. Forcemapping and . Setscanpixels, 16) ForceMapping.setScanOffset(0, 0) #coordinates where the force map is going to be obtained ForceMapping, vol.16

, ForceSpectroscopy.setAutosave(1) ForceSpectroscopy.setOutputDirectory(path+"/Cell"+str(g) + '--' + str

. Forcespectroscopy, . Fastlength, . Slowlength, . Xgridcenter, and N. Ygridcenter, NumSlowPoints, angle) Scanner.approachPiezo() #Iterating through the measurement grid ForceSpectroscopy.startScansPerPosition(1) Scanner.retractPiezo() #print "Indenting point

, Exp2Tre <-subset(Exp1, select = c

. &lt;-filteru1, Cells %>% filter(filterU1.Cells$Clust == 1)

, StatasU1.2 <-filterU1.Cells %>% filter(filterU1.Cells$Clust == 2)

. &lt;-filteru1, Cells %>% filter(filterU1.Cells$Clust == 3)

, StatasT1.1 <-filterT1.Cells %>% filter(filterT1.Cells$Clust == 1)

, StatasT1.2 <-filterT1.Cells %>% filter(filterT1.Cells$Clust == 2)

. &lt;-filtert1, Cells %>% filter(filterT1.Cells$Clust ==, vol.3, p.2

, StatasU2.2 <-filterU2.Cells %>% filter(filterU2.Cells$Clust == 1)

, StatasU2.2 <-filterU2.Cells %>% filter(filterU2.Cells$Clust == 2)

, StatasT2.1 <-filterT2.Cells %>% filter(filterT2.Cells$Clust == 1)

, StatasT2.2 <-filterT2.Cells %>% filter(filterT2.Cells$Clust == 2) #ANOVA test Slope, vol.-------------------------------------------------------------------------------

&. Temp,

, Set1.Sl <-cbind(filterT1.Cells,Temp) Temp <-head(filterU2.Cells, nrow(filterT2.Cells))

, Set2.Sl <-cbind(filterT2.Cells,Temp)

. Oneway1 and . Info-&lt;-set1, TSlR30")) %>% gather(SlopeType, SlopeVal, USlR30, TSlR30) Oneway2.info <-Set2.Sl %>% subset(select = c, TSlR30")) %>% gather(SlopeType, SlopeVal, USlR30, TSlR30) $SlopeType <-plyr::revalue(Oneway1.info$SlopeType , c

. Oneway2 and . Info$slopetype-&lt;-plyr, USlR30" = "Native, revalue(Oneway2.info$SlopeType , c

. Slopetype, ;. Slopeval, and . Xlab, #0099FF")) + theme(text = element_text(size = 18)) + ylab, fill = SlopeType)) + geom_boxplot(colour = "blue, vol.#Anova adhesion---------------------------------------------------------------------------------

&. Temp,

&. Ad,

&. Temp2,

, Wells" #Re-arranging the variables Set1.AnovaAdh1 <-Set1.Ad %>% subset(select = c("UAdhesion, Set2.Ad <-cbind(AdhUn2Filtered.Cells,Temp2) colnames(Set2.Ad)[14] <-"TAdhesion" colnames(Set2.Ad

&. Anovaadh2, Adhesion")) %>% gather(AdhGroup, AdhesionVal, Uadhesion, Adhesion) #Renaming AdhesionGroup

. Anovaadh1$adhgroup-&lt;-plyr, UAdhesion" = "Native, revalue(Set1.AnovaAdh1$AdhGroup, c

. Anovaadh2$adhgroup-&lt;-plyr, Uadhesion" = "Native, revalue(Set2.AnovaAdh2$AdhGroup, c

, Treated")) + geom_signif(comparisons = list(c("Native, + scale_fill_discrete(breaks = c("Native

, AnovaAdh1, width = 6, height = 4, dpi = 200) compstr <-paste("Well", toString(j), sep =, Images/ANOVA-Adh1.svg

=. Selectedwell and . Na, omit(filter(AdhT2Filtered.Cells, TWells == compstr)) averageTA = mean(as.numeric(SelectedWell$Adhesion

, medianTA = median(as.numeric(SelectedWell$Adhesion))

. Avemediantadh2, <-list(compstr, averageTA, medianTA) for adhesion bw <-(2 * IQR(AveMedianUAdh2

, ) * 100), binwidth = bw, color = "#FF3333", fill = "#993300") + theme(text = element_text(size = 16)) + ylab("Frequency %") + xlab("Adhesion [N]") + labs(title = "Histogram of the average adhesion values per cell, subtitle = "Native C. albicans cells") ggsave("Images/CellSlAverage_UA2.png

, ) * 100), binwidth = bw, color = "#99CCFF", fill = "#3333FF") + theme(text = element_text(size = 16)) + ylab("Frequency %") + xlab("Adhesion [N]") + labs(title = "Histogram of the median adhesion values per cell, subtitle = "Native C. albicans cells") ggsave("Images/CellSlMedian_UA2.png

, )/sum(..count..) * 100), binwidth = bw, color = "#FF3333", fill = "#993300") + theme(text = element_text(size = 16)) + ylab

, CellSlAverageTA2, width = 7.5, height = 5, dpi = 300) bw <-(2 * IQR(AveMedianTAdh2

, )/sum(..count..) * 100), binwidth = bw, color = "#99CCFF", fill = "#3333FF") + theme(text = element_text(size = 16)) + ylab("Frequency %") + xlab("Adhesion [N]") + labs(title = "Histogram of the median adhesion values per cell

, Images/CellSlMedian_TA2.png