D. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, and S. W. Wilkins, Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object, J. Microsc, vol.206, issue.1, pp.33-40, 2002.

D. Gabor, A New Microscopic Principle, Nature, vol.161, issue.4098, pp.777-778, 1948.

T. Weitkamp, A. Diaz, C. David, F. Pfeiffer, M. Stampanoni et al., X-ray phase imaging with a grating interferometer, Opt. Express, vol.13, issue.16, p.6296, 2005.

F. Zernike, Das Phasenkontrastverfahren bei der mikroskopischen Beobachtung, Z. Techn. Physik, vol.16, pp.454-457, 1935.

G. Schmahl, D. Rudolph, G. Schneider, P. Guttmann, and B. Niemann, Phase contrast X-ray microscopy studies, Optik, vol.97, pp.181-182, 1994.

M. Awaji, Y. Suzuki, A. Takeuchi, H. Takano, N. Kamijo et al., Zernike-type X-ray imaging microscopy at 25 keV with Fresnel zone plate optics, J. Synchrotron Rad, vol.9, issue.3, pp.125-127, 2002.

U. Neuhäusler, G. Schneider, W. Ludwig, M. A. Meyer, E. Zschech et al., X-ray microscopy in Zernike phase contrast mode at 4 keV photon energy with 60 nm resolution, J. Phys. D: Appl. Phys, vol.36, issue.10A, pp.79-82, 2003.

M. Stampanoni, R. Mokso, F. Marone, J. Vila-comamala, S. Gorelick et al., Phase-contrast tomography at the nanoscale using hard x rays, Phys. Rev. B, vol.81, issue.14, p.140105, 2010.

A. Bravin, P. Coan, and P. Suortti, X-ray phase-contrast imaging: From pre-clinical applications towards clinics, Phys. Med. Biol, vol.58, issue.1, pp.1-35, 2013.

A. Khimchenko, C. Bikis, A. Pacureanu, S. E. Hieber, P. Thalmann et al., Hard X-Ray Nanoholotomography: Large-Scale, Label-Free, 3D Neuroimaging beyond Optical Limit, Adv. Sci, vol.5, issue.6, p.1700694, 2018.

M. Töpperwien, F. Van-der-meer, C. Stadelmann, and T. Salditt, Correlative x-ray phase-contrast tomography and histology of human brain tissue affected by Alzheimer's disease, NeuroImage, vol.210, p.116523, 2020.

M. Töpperwien, F. Van-der-meer, C. Stadelmann, and T. Salditt, Three-dimensional virtual histology of human cerebellum by X-ray phase-contrast tomography, Proc. Natl. Acad. Sci. U. S. A, vol.115, issue.27, pp.6940-6945, 2018.

A. Pacureanu, J. Maniates-selvin, A. T. Kuan, L. A. Thomas, C. Chen et al., Dense neuronal reconstruction through x-ray holographic nano-tomography, bioRxiv, 2019.

L. Massimi, I. Bukreeva, G. Santamaria, M. Fratini, A. Corbelli et al., Exploring Alzheimer's disease mouse brain through X-ray phase contrast tomography: From the cell to the organ, NeuroImage, vol.184, pp.490-495, 2019.

A. Cedola, A. Bravin, I. Bukreeva, M. Fratini, A. Pacureanu et al., X-Ray Phase Contrast Tomography Reveals Early Vascular Alterations and Neuronal Loss in a Multiple Sclerosis Model, Sci. Rep, vol.7, issue.1, p.5890, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01691867

P. Cloetens, W. Ludwig, J. Baruchel, D. Van-dyck, J. Van-landuyt et al., Holotomography: Quantitative phase tomography with micrometer resolution using hard synchrotron radiation x rays, Appl. Phys. Lett, vol.75, pp.2912-2914, 1999.

M. Busse, M. Müller, M. A. Kimm, S. Ferstl, S. Allner et al., Threedimensional virtual histology enabled through cytoplasm-specific X-ray stain for microscopic and nanoscopic computed tomography, Proc. Natl. Acad. Sci. U. S. A, vol.115, issue.10, pp.2293-2298, 2018.

C. C. Chien, C. C. Cheng, H. H. Chen, Y. Hwu, Y. S. Chu et al., X-ray microscopy and tomography detect the accumulation of bare and PEG-coated gold nanoparticles in normal and tumor mouse tissues, Anal. Bioanal. Chem, vol.404, issue.5, pp.1287-1296, 2012.

R. Mokso, L. Quaroni, F. Marone, S. Irvine, J. Vila-comamala et al., X-ray mosaic nanotomography of large microorganisms, J. Struct. Biol, vol.177, issue.2, pp.233-238, 2012.

J. C. Andrews, F. Meirer, Y. Liu, Z. Mester, and P. Pianetta, Transmission x-ray microscopy for full-field nano imaging of biomaterials, Microsc. Res. Tech, vol.74, issue.7, pp.671-681, 2011.

E. Larsson, D. Gürsoy, F. De-carlo, E. Lilleodden, M. Storm et al., Nanoporous gold: a hierarchical and multiscale 3D test pattern for characterizing X-ray nano-tomography systems, J. Synchrotron Radiat, vol.26, issue.1, pp.194-204, 2019.

J. J. Lombardo, R. A. Ristau, W. M. Harris, and W. K. Chiu, Focused ion beam preparation of samples for X-ray nanotomography, J. Synchrotron Radiat, vol.19, issue.5, pp.789-796, 2012.

N. E. Buglak, J. Lucitti, P. Ariel, S. Maiocchi, J. Miller et al., Light sheet fluorescence microscopy as a new method for unbiased three-dimensional analysis of vascular injury, Cardiovasc. Res, 2020.

J. F. Dekkers, M. Alieva, L. M. Wellens, H. C. Ariese, P. R. Jamieson et al., High-resolution 3d imaging of fixed and cleared organoids, Nat. Protoc, vol.14, issue.6, pp.1756-1771, 2019.

M. Sivaguru, G. Fried, B. S. Sivaguru, V. A. Sivaguru, X. Lu et al., Cardiac muscle organization revealed in 3-d by imaging whole-mount mouse hearts using twophoton fluorescence and confocal microscopy, BioTechniques, vol.59, issue.5, pp.295-308, 2015.

L. Silvestri, A. Bria, L. Sacconi, G. Iannello, and F. S. Pavone, Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain, Opt. Express, vol.20, issue.18, pp.20582-20598, 2012.

I. Costantini, R. Cicchi, L. Silvestri, F. Vanzi, and F. S. Pavone, In-vivo and ex-vivo optical clearing methods for biological tissues: review, Biomed. Opt. Express, vol.10, issue.10, pp.5251-5267, 2019.

X. Zhu, L. Huang, Y. Zheng, Y. Song, Q. Xu et al., Ultrafast optical clearing method for three-dimensional imaging with cellular resolution, Proc. Natl. Acad. Sci, vol.116, pp.11480-11489, 2019.

A. Kazarine, K. Kolosova, A. A. Gopal, H. Wang, R. Tahara et al., Multimodal virtual histology of rabbit vocal folds by nonlinear microscopy and nano computed tomography, Biomed. Opt. Express, vol.10, issue.3, pp.1151-1164, 2019.

M. A. Le-gros, G. Mcdermott, and C. A. Larabell, X-ray tomography of whole cells, Curr. Opin. Struct. Biol, vol.15, issue.5, pp.593-600, 2005.

G. Mcdermott, M. A. Le-gros, C. G. Knoechel, M. Uchida, and C. A. Larabell, Soft X-ray Tomography and Cryogenic Light Microscopy: The Cool Combination in Cellular Imaging, Trends Cell Biol, vol.19, issue.11, pp.587-595, 2009.

C. Larabell and K. A. Nugent, Imaging Cellular Architecture with X-rays, Curr. Opin. Struct. Biol, vol.20, issue.5, pp.623-631, 2010.

I. Greving, F. Wilde, M. Ogurreck, J. Herzen, J. U. Hammel et al., P05 imaging beamline at PETRA III: first results, Dev. X-Ray Tomogr. IX, vol.9212, p.92120, 2014.

M. Ogurreck, F. Wilde, J. Herzen, F. Beckmann, V. Nazmov et al., The nanotomography endstation at the PETRA III imaging beamline, J. Phys.: Conf. Ser, vol.425, issue.18, p.182002, 2013.

I. Vartiainen, C. Holzner, I. Mohacsi, P. Karvinen, A. Diaz et al., Artifact characterization and reduction in scanning X-ray Zernike phase contrast microscopy, Opt. Express, vol.23, issue.10, pp.13278-13294, 2015.

P. Thurner, F. Beckmann, and B. Müller, An optimization procedure for spatial and density resolution in hard X-ray micro-computed tomography, Nucl. Instrum. Methods Phys. Res., Sect. B, vol.225, issue.4, pp.599-603, 2004.

B. Münch, P. Trtik, F. Marone, and M. Stampanoni, Stripe and ring artifact removal with combined wavelet -Fourier filtering, Opt. Express, vol.17, issue.10, p.8567, 2009.

D. Gürsoy, F. De-carlo, X. Xiao, and C. Jacobsen, TomoPy: A framework for the analysis of synchrotron tomographic data, J. Synchrotron Radiat, vol.21, issue.5, pp.1188-1193, 2014.

B. A. Dowd, G. H. Campbell, R. B. Marr, V. V. Nagarkar, S. V. Tipnis et al., Developments in synchrotron x-ray computed microtomography at the National Synchrotron Light Source, Dev. X-Ray Tomogr. II, vol.3772, pp.224-236, 1999.

J. Schindelin, I. Arganda-carreras, E. Frise, V. Kaynig, M. Longair et al., Fiji: An open-source platform for biological-image analysis, Nat. Methods, vol.9, issue.7, pp.676-682, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-02616466

R. P. Nieuwenhuizen, K. A. Lidke, M. Bates, D. L. Puig, D. Grünwald et al., Measuring image resolution in optical nanoscopy, Nat. Methods, vol.10, issue.6, pp.557-562, 2013.

M. Van-heel and M. Schatz, Fourier shell correlation threshold criteria, J. Struct. Biol, vol.151, issue.3, pp.250-262, 2005.

A. Miettinen, I. V. Oikonomidis, A. Bonnin, and M. Stampanoni, Nrstitcher: non-rigid stitching of terapixel-scale volumetric images, Bioinformatics, vol.35, issue.24, pp.5290-5297, 2019.

C. Holzner, M. Feser, S. Vogt, B. Hornberger, S. B. Baines et al., Zernike phase contrast in scanning microscopy with X-rays, Nat. Phys, vol.6, issue.11, pp.883-887, 2010.

J. L. Zhuo and X. C. Li, Proximal Nephron, Compr. Physiol, vol.3, issue.3, pp.1079-1123, 2013.

A. R. Subramanya and D. H. Ellison, Distal convoluted tubule, Clin. J. Am. Soc. Nephrol, vol.9, issue.12, pp.2147-2163, 2014.

J. A. Mccormick and D. H. Ellison-division, The Distal Convoluted Tubule, vol.5, pp.45-98, 2015.

A. G. Booth and A. J. Kenny, Proteins o the kidney microvillus membrane, Biochem. J, vol.159, issue.2, pp.395-407, 1976.

A. Karageorgis, S. Dufort, L. Sancey, M. Henry, S. Hirsjärvi et al., An MRI-based classification scheme to predict passive access of 5 to 50-nm large nanoparticles to tumors, Sci. Rep, vol.6, issue.1, p.21417, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01388813