A. E. Abdel-hakim and A. A. Farag, CSIFT : A SIFT Descriptor with Color Invariant Characteristics, vol.2, 2006.

A. Alexandre, O. Raphael, and V. Pierre, FREAK : Fast Retina Keypoint, IEEE Conference on Computer Vision and Pattern Recognition, pp.510-517, 2012.

A. Pablo, A. Bartoli, D. Andrew, J. Kaze-features, and . Springerlink, , pp.214-227, 2012.

A. Pablo, N. Jesus, and B. Adrien, Fast explicit diffusion for accelerated features in nonlinear scale spaces, Proceedings of the British Machine Vision Conference, 2013.

A. H. Andersen and A. C. Kak, Simultaneous Algebraic Reconstruction Technique (SART) : A superior implementation of the ART algorithm, Ultrasonic Imaging, vol.6, issue.1, pp.81-94, 1984.

K. Batenburg, S. Joost, and . Jan, DART : A Practical Reconstruction Algorithm for Discrete Tomography, IEEE Trans. Image Process, vol.20, issue.9, pp.2542-2553, 2011.

B. Herbert, E. Andreas, T. Tinne, . Van-gool, and . Luc, Speeded-Up Robust Features (SURF), Comput. Vision Image Understanding, vol.110, issue.3, pp.346-359, 2008.

A. Béché, B. Goris, B. Freitag, and J. Verbeeck, Development of a fast electromagnetic beam blanker for compressed sensing in scanning transmission electron microscopy, Appl. Phys. Lett, vol.108, issue.9, p.93103, 2016.

J. S. Beis and D. G. Lowe, Shape indexing using approximate nearest-neighbour search in highdimensional spaces, IEEE, 1997.

G. Bicer-tekin, D. Doga, K. Vincent, S. Rajkumar, . William et al., Trace : a high-throughput tomographic reconstruction engine for large-scale datasets, Adv. Struct. Chem. Imag, vol.3, issue.1, pp.1-10, 2017.

G. Bradski, The OpenCV Library. Dr. Dobb's Journal of Software Tools, 2000.

L. Brown, Recognising panoramas. IEEE, 2003.

B. Matthew, L. David, and G. , Automatic Panoramic Image Stitching using Invariant Features, Int. J. Comput. Vision, vol.74, issue.1, pp.59-73, 2007.

B. James, P. , R. Quentin, G. Bryant, B. Nigel et al., High-resolution low-dose scanning transmission electron microscopy, J. Electron Microsc, vol.59, issue.2, pp.103-112, 2009.

H. Burger-martin, S. Lin, and . Carola-bibiane, Cahn-Hilliard Inpainting and a Generalization for Grayvalue Images, SIAM J. Imag. Sci, vol.2, issue.4, pp.1129-1167, 2009.

C. Emmanuel, J. Romberg-justin, K. , and T. Terence, Stable signal recovery from incomplete and inaccurate measurements, Commun. Pure Appl. Math, vol.59, issue.8, pp.1207-1223, 2006.

C. Daniel, S. Margot, A. Ashraf, F. Achilleas, and S. Alignator, A GPU powered software package for robust fiducial-less alignment of cryo tilt-series, J. Struct. Biol, vol.170, issue.1, pp.117-126, 2010.

C. Tony, F. , and S. Jianhong, Variational image inpainting, Commun. Pure Appl. Math, vol.58, issue.5, pp.579-619, 2005.

C. Delei, G. Bart, B. Folkert, M. Hamed-heidari, and B. Sara, Batenburg Kees Joost, de With Gijsbertus, and Friedrich Heiner. The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections, Ultramicroscopy, vol.147, pp.137-148, 2014.

C. Christian, K. Mathieu, and S. Odile, Electron Energy Loss Spectroscopy imaging of surface plasmons at the nanometer scale, Ultramicroscopy, vol.162, pp.1-24, 2016.

A. V. Crewe and J. Wall, A scanning microscope with 5 Å resolution, J. Mol. Biol, vol.48, issue.3, pp.375-393, 1970.

T. Da-cunha-marcel-menezes-lyra, M. Sylvain, W. Cédric, O. Ting-di, G. Richard et al., Overview of chemical imaging methods to address biological questions, Micron, vol.84, pp.23-36, 2016.

D. Radostin and N. Kuniaki, Transmission electron microscopy with Zernike phase plate, Ultramicroscopy, vol.88, issue.4, pp.243-252, 2001.

D. Radostin and N. Kuniaki, Optimizing the phase shift and the cut-on periodicity of phase plates for TEM, Ultramicroscopy, vol.111, issue.8, pp.1305-1315, 2011.

G. Danev-radostin, M. Robert, and N. Kuniaki, Practical factors affecting the performance of a thin-film phase plate for transmission electron microscopy, Ultramicroscopy, vol.109, issue.4, pp.312-325, 2009.

B. Danev-radostin, K. Bart, P. Maryam, M. Jürgen, and B. Wolfgang, Volta potential phase plate for in-focus phase contrast transmission electron microscopy, Proc. Natl. Acad. Sci. U.S.A, vol.111, issue.44, pp.15635-15640, 2014.

P. Donnadieu, S. Lazar, G. A. Botton, I. Pignot-paintrand, M. Reynolds et al., Seeing structures and measuring properties with transmission electron microscopy images : A simple combination to study size effects in nanoparticle systems, Appl. Phys. Lett, vol.94, issue.26, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00413874

D. L. Donoho, Compressed sensing, IEEE Transactions on Information Theory, vol.52, 2006.
URL : https://hal.archives-ouvertes.fr/inria-00369486

J. Dubochet, J. Lepault, . Cryo-electron, . Microscopy, and . Vitrified-water, J. Phys. Colloques, vol.45, issue.C7, 1984.

D. Jacques, A. Marc, C. Jiin-ju, H. Jean-claude, L. Jean et al., Cryo-electron microscopy of vitrified specimens, Q. Rev. Biophys, vol.21, issue.2, pp.129-228, 1988.

C. J. Edgcombe, A. Ionescu, J. C. Loudon, A. M. Blackburn, H. Kurebayashi et al., Characterisation of ferromagnetic rings for Zernike phase plates using the Aharonov-Bohm effect, Ultramicroscopy, vol.120, pp.78-85, 2012.

R. F. Egerton, P. Li, and M. Malac, Radiation damage in the TEM and SEM, Micron, vol.35, issue.6, pp.399-409, 2004.

F. Martin, A. , B. Robert, and C. , Random sample consensus : a paradigm for model fitting with applications to image analysis and automated cartography, Commun. ACM, vol.24, issue.6, pp.381-395, 1981.

F. Nicole, O. Marco, H. Simon, G. Björn, D. Levin et al., Gerthsen Dagmar, and Schröder Rasmus R. In-Focus Electrostatic Zach Phase Plate Imaging for Transmission Electron Microscopy with Tunable Phase Contrast of Frozen Hydrated Biological Samples, Microsc. Microanal, vol.20, issue.1, pp.175-183, 2014.

G. Damien, Robust smoothing of gridded data in one and higher dimensions with missing values, Computational Statistics & Data Analysis, vol.54, issue.4, pp.1167-1178, 2010.

G. Peter, Iterative methods for the three-dimensional reconstruction of an object from projections, J. Theor. Biol, vol.36, issue.1, pp.105-117, 1972.

G. Iryna, L. David, and G. , What and Where : 3D Object Recognition with Accurate Pose. SpringerLink, pp.67-82, 2006.

G. Richard, B. Robert, H. Gabor, and T. , Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and X-ray photography, J. Theor. Biol, vol.29, issue.3, pp.471-481, 1970.

G. Matthew, D. , C. Wojciech, A. Maria, A. et al., Compressed Sensing Electron Tomography for Determining Biological Structure. Sci. Rep, vol.6, p.27614, 2016.

H. Renmin, Z. Fa, W. Xiaohua, F. Jose-jesus, S. Fei et al., A markerfree automatic alignment method based on scale-invariant features, J. Struct. Biol, vol.186, issue.1, pp.167-180, 2014.

H. Eric, Cellular Imaging, 2018.

I. Takashi, Axoneme Structure from Motile Cilia, Cold Spring Harbor Perspect. Biol, vol.9, issue.1, p.28076, 2017.

. I??k?ahin, Comparative Evaluation of Well-known Feature Detectors and Descriptors. International Journal of Applied Mathematics Electronics and Computers, vol.3, issue.1, pp.1-6, 2015.

, Measuring probe convergent angle in stem mode and take off angle in haadf, JEOL, 2003.

K. Konstantin, B. Adrian, B. Frederick, and P. Adrian, GPU implementation of cross-correlation for image generation in real time, 9th International Conference on Signal Processing and Communication Systems (ICSPCS), pp.1-6, 2015.

K. Yan and R. Sukthankar, PCA-SIFT : a more distinctive representation for local image descriptors, vol.2, 2004.

C. Kim-min-woo, Y. Jiyoung, L. K. Liu, H. Eun, Y. Sung-sik et al., Cryo-electron microscopy single particle reconstruction of virus particles using compressed sensing theory, Computational Imaging V, vol.6498, p.64981, 2007.

T. Koch-christoph, Towards full-resolution inline electron holography, Micron, vol.63, pp.69-75, 2014.

L. Lambert, T. E. Mulvey, and . Ruska, Designer Extraordinaire of the Electron Microscope : A Memoir, Advances in Imaging and Electron Physics, vol.95, pp.2-62, 1906.

L. Ivan and L. Tony, Local Descriptors for Spatio-temporal Recognition. SpringerLink, pp.91-103, 2004.

S. Leary-rowan, M. Zineb, A. Paul, H. Daniel, and J. , Compressed sensing electron tomography, Ultramicroscopy, vol.131, pp.70-91, 2013.

L. Stefan, C. Margarita, S. Roland, and Y. Brisk, Binary Robust invariant scalable keypoints. 2011 International Conference on Computer Vision, pp.2548-2555, 2011.

L. Suresh, K. , and X. Yongqin, GSIFT : geometric scale invariant feature transform for terrain data, Vision Geometry XIV, vol.6066, p.60660, 2006.

L. David and G. , Distinctive Image Features from Scale-Invariant Keypoints, Int. J. Comput. Vision, vol.60, issue.2, pp.91-110, 2004.

M. Michael, H. Chyongere, L. Eric, M. David, and M. Sohei, Practical Experience with Hole-Free Phase Plates for Cryo Electron Microscopy, Microsc. Microanal, vol.22, issue.6, pp.1316-1328, 2014.

M. David and N. , Fiducial Marker and Hybrid Alignment Methods for Single-and Doubleaxis Tomography. SpringerLink, pp.163-185, 2007.

J. Matas, O. Chum, M. Urban, and T. Pajdla, Robust wide-baseline stereo from maximally stable extremal regions, Image Vision Comput, vol.22, issue.10, pp.761-767, 2004.

M. Takao and T. Akira, The phase constancy of electron waves traveling through Boersch's electrostatic phase plate, Ultramicroscopy, vol.63, issue.1, pp.5-10, 1996.

M. Cédric, B. Thomas, S. Sanchez, and M. Sergio, TomoJ : tomography software for three-dimensional reconstruction in transmission electron microscopy, BMC Bioinf, vol.8, issue.1, pp.1-9, 2007.

M. Cédric, A. Nicolas, C. Marcel, O. Tetsuo, S. Carlos et al., Three-Dimensional Chemical Mapping by EFTEM-TomoJ Including Improvement of SNR by PCA and ART Reconstruction of Volume by Noise Suppression. Microsc. Microanal, vol.19, pp.1669-1677, 2013.

P. A. Midgley and M. Weyland, 3D electron microscopy in the physical sciences : the development of Z-contrast and EFTEM tomography, Ultramicroscopy, vol.96, issue.3, pp.413-431, 2003.

P. A. Midgley, M. Weyland, T. J. Yates, I. Arslan, R. E. Dunin-borkowski et al., Nanoscale scanning transmission electron tomography, J. Microsc, vol.223, issue.3, pp.185-190, 2006.

M. Jean, -. Michel, and Y. Guoshen, ASIFT : A New Framework for Fully Affine Invariant Image Comparison, SIAM J. Imag. Sci, vol.2, issue.2, pp.438-469, 2009.

N. Kuniaki and D. Radostin, Phase contrast electron microscopy : development of thin-film phase plates and biological applications, Philosophical Transactions of the Royal Society B : Biological Sciences, 2008.

P. Chad, G. , and W. Mark, Basal body assembly in ciliates : the power of numbers, Traffic, vol.10, issue.5, p.461, 2009.

P. Stephen, J. , N. Peter, and D. , Scanning Transmission Electron Microscopy | Springer-Link, 2011.

R. Johann, On the determination of functions from their integral values along certain manifolds, IEEE Trans. Med. Imaging, vol.5, issue.4, pp.170-176, 1986.

R. Ludwig and K. Helmut, Transmission Electron Microscopy -Physics of Image Formation | Ludwig Reimer | Springer, 2008.

R. Edward and D. Tom, Machine Learning for High-Speed Corner Detection. Sprin-gerLink, pp.430-443, 2006.

R. Ethan, R. Vincent, K. Kurt, and B. Gary, ORB : An efficient alternative to SIFT or SURF, International Conference on Computer Vision, pp.2564-2571, 2011.

S. Paul, A. Saad, and S. Mubarak, A 3-dimensional sift descriptor and its application to action recognition, 2007.

S. Se, D. Lowe, and J. Little, Vision-based mobile robot localization and mapping using scaleinvariant features, vol.2, 2001.

C. E. Shannon, Communication in the Presence of Noise, Proc. IRE, vol.37, pp.10-21, 1949.

S. Sanchez, M. Cédric, E. Matthias, J. R. Bilbao-castro, R. Hegerl et al., Marker-free image registration of electron tomography tiltseries, BMC Bioinf, vol.10, issue.1, p.124, 2009.

A. A. Sousa, M. F. Hohmann-marriott, G. Zhang, and R. D. Leapman, Monte Carlo electrontrajectory simulations in bright-field and dark-field STEM : Implications for tomography of thick biological sections, Ultramicroscopy, vol.109, issue.3, pp.213-221, 2009.

. Sternberg, Biomedical Image Processing. Computer, vol.16, issue.1, pp.22-34, 1983.

T. Ahmad, P. Baghaie-ahmadreza, K. Andrew, B. Holz-jessica, D. et al., A comparative study on the application of SIFT, SURF, BRIEF and ORB for 3D surface reconstruction of electron microscopy images, Computer Methods in Biomechanics and Biomedical Engineering : Imaging & Visualization, vol.6, issue.1, pp.17-30, 2018.

S. A. Tareen, Z. Saleem, . Sift, . Surf, A. Kaze et al., International Conference on Computing, Mathematics and Engineering Technologies (iCo-MET), pp.1-10, 2018.

T. Anne-marie, L. Michel, and A. Anne, Paramecium tetraurelia basal body structure. Cilia, vol.5, pp.1-6, 2015.

A. N. Tikhonov, Solution of Incorrectly Formulated Problems and the Regularization Method, 1963.

T. Sylvain, T. Anne-marie, M. Sergio, and B. Philippe, STEM tomography analysis of the trypanosome transition zone, J. Struct. Biol, vol.202, issue.1, pp.51-60, 2018.

A. Verguet, C. Messaoudi, C. O. Sorzano, and M. S. , Alignment of Tilt Series. SpringerLink, pp.183-207, 2018.

M. Verguet-amandine, M. Cédric, D. Sergio, and . Patricia, An ImageJ tool for simplified post-treatment of TEM phase contrast images (SPCI), vol.121, pp.90-98, 2019.

, Z. Angew. Phys, vol.109, issue.9, pp.553-572, 1938.

W. Ge and J. Ming, Ordered-subset simultaneous algebraic reconstruction techniques (OS-SART), J. X-Ray Sci. Technol, vol.12, issue.3, pp.169-177, 2004.

W. David, B. Carter, C. Barry-;-|-david, B. Williams, and . Springer, Transmission Electron Microscopy -A Textbook for Materials Science, 2009.

W. Hanspeter, T. Kenneth, and A. , Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography, Ultramicroscopy, vol.106, issue.3, pp.240-254, 2006.

H. Wolf-sharon-grayer, E. Lothar, and . Michael, Cryo-scanning transmission electron tomography of vitrified cells, Nat. Methods, vol.11, issue.4, p.423, 2014.

C. Wu-jian, S. Zhiming, S. Victor, S. Zhao-pengpeng, G. Dongliang et al., A Comparative Study of SIFT and its Variants, Measurement Science Review, vol.13, issue.3, pp.122-131, 2013.

F. Zernike, Phase contrast, a new method for the microscopic observation of transparent objects, Physica, vol.9, issue.7, pp.686-698, 1942.

D. Zhou, X. Shen, and D. W. , Image zooming using directional cubic convolution interpolation, IET Image Proc, vol.6, issue.6, pp.627-634, 2012.

P. Alcantarilla, A. Bartoli, and A. J. Davison, KAZE Features. SpringerLink, 2012.

P. Alcantarilla, J. Nuevo, and A. Bartoli, Fast explicit diffusion for accelerated features in nonlinear scale spaces, Proceedings of the British Machine Vision Conference, 2013.

F. Amat, F. Moussavi, L. R. Comolli, G. Elidan, K. H. Downing et al., Markov random field based automatic image alignment for electron tomography, J. Struct. Biol, vol.161, pp.260-275, 2008.

S. Audet, , 2015.

H. Bay, A. Ess, T. Tuytelaars, and L. Van-gool, Speeded-Up Robust Features (SURF). Comput. Vision Image Understanding 110, pp.346-359, 2008.

J. S. Beis and D. G. Lowe, Shape indexing using approximate nearest-neighbour search in high-dimensional spaces, IEEE, 1997.

G. Bradski, The OpenCV Library. Dr. Dobb's Journal of Software Tools, 2000.

S. Brandt, J. Heikkonen, and P. Engelhardt, Automatic Alignment of Transmission Electron Microscope Tilt Series without Fiducial Markers, J. Struct. Biol, vol.136, pp.201-213, 2001.

S. S. Brandt and J. Heikkonen, A fully automatic alignment of electron tomography images without fiducial markers, Proceedings of the IAPR Conference on Machine Vision Applications (IAPR MVA 2000), pp.307-310, 2000.

J. Buisson and P. Bastin, Flagellum Structure and Function in Trypanosomes, pp.63-86, 2010.

M. Calonder, V. Lepetit, C. Strecha, and P. Fua, BRIEF: Binary Robust Independent Elementary Features. SpringerLink, 2010.

B. I. Carbajal-gonzález, T. Heuser, X. Fu, J. Lin, B. W. Smith et al., Conserved structural motifs in the central pair complex of eukaryotic flagella, Cytoskeleton, vol.70, pp.101-120, 2013.

D. Castaño-díez, M. Scheffer, A. Al-amoudi, and A. S. Frangakis, Alignator: A GPU powered software package for robust fiducial-less alignment of cryo tilt-series, J. Struct. Biol, vol.170, pp.117-126, 2010.

R. Han, F. Zhang, X. Wan, J. J. Fernández, F. Sun et al., A marker-free automatic alignment method based on scale-invariant features, J. Struct. Biol, vol.186, pp.167-180, 2014.

H. Huang, L. Lu, B. Yan, and J. Chen, A new scale invariant feature detector and modified SURF descriptor, Sixth International Conference on Natural Computation, vol.7, pp.3734-3738, 2010.

O. Kovtun, N. Leneva, Y. S. Bykov, N. Ariotti, R. D. Teasdale et al., Structure of the membrane-assembled retromer coat determined by cryo-electron tomography, Nature, vol.561, pp.561-564, 2018.

A. Y. Koyfman, M. F. Schmid, L. Gheiratmand, C. J. Fu, H. A. Khant et al., Structure of Trypanosoma brucei flagellum accounts for its bihelical motion, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.11105-11108, 2011.

S. Leutenegger, M. Chli, and R. Y. Siegwart, BRISK: Binary Robust invariant scalable keypoints, International Conference on Computer Vision, 2011.

D. G. Lowe, Distinctive Image Features from Scale-Invariant Keypoints, Int. J. Comput. Vision, vol.60, pp.91-110, 2004.

E. Mair, G. D. Hager, D. Burschka, M. Suppa, and G. Hirzinger, Adaptive and Generic Corner Detection Based on the Accelerated Segment Test. SpringerLink, p.183, 2010.

D. N. Mastronarde, Fiducial Marker and Hybrid Alignment Methods for Single-and Double-axis Tomography. SpringerLink, 2007.

D. N. Mastronarde and S. R. Held, Automated tilt series alignment and tomographic reconstruction in IMOD, J. Struct. Biol, vol.197, pp.102-113, 2017.

S. Mattei, A. Tan, B. Glass, B. Müller, H. G. Kräusslich et al., High-resolution structures of HIV-1 Gag cleavage mutants determine structural switch for virus maturation, Proc. Natl. Acad. Sci. U.S.A, vol.115, 2018.

C. Messaoudi, Online; accessed 27, 2011.

C. Messaoudi, T. Boudier, C. O. Sorzano, and S. Marco, TomoJ: tomography software for threedimensional reconstruction in transmission electron microscopy, BMC Bioinf, vol.8, p.288, 2007.

O. Miksik and K. Mikolajczyk, Evaluation of local detectors and descriptors for fast feature matching, Proceedings of the 21st International Conference on Pattern Recognition (ICPR2012), pp.2681-2684, 2012.

D. R. Mitchell, Orientation of the central pair complex during flagellar bend formation in Chlamydomonas, Cell Motil. Cytoskeleton, vol.56, pp.120-129, 2003.

D. R. Mitchell and B. Smith, Chapter 13 -Analysis of the Central Pair Microtubule Complex in Chlamydomonas reinhardtii, Methods in Cell Biology, vol.92, pp.92013-92019, 2009.

E. Rosten and T. Drummond, Machine Learning for High-Speed Corner Detection. SpringerLink, p.430, 2006.

E. Rublee, V. Rabaud, K. Konolige, and G. Bradski, ORB: An efficient alternative to SIFT or SURF, International Conference on Computer Vision, 2011.

W. O. Saxton, W. Baumeister, and M. Hahn, Three-dimensional reconstruction of imperfect twodimensional crystals, Ultramicroscopy, vol.13, pp.57-70, 1984.

F. A. Shah, B. R. Johansson, P. Thomsen, and A. Palmquist, Ultrastructural evaluation of shrinkage artefacts induced by fixatives and embedding resins on osteocyte processes and pericellular space dimensions, J. Biomed. Mater. Res. Part A, vol.103, pp.1565-1576, 2015.

C. O. Sorzano, C. Messaoudi, M. Eibauer, J. Bilbao-castro, R. Hegerl et al., Marker-free image registration of electron tomography tilt-series, BMC Bioinf, vol.10, p.124, 2009.

S. Trépout, A. M. Tassin, S. Marco, and P. Bastin, STEM tomography analysis of the trypanosome transition zone, J. Struct. Biol, vol.202, pp.51-60, 2018.

G. Wang and M. Jiang, Ordered-subset simultaneous algebraic reconstruction techniques (OS-SART), 2004.

J. , X. Sci, ;. P. Lazar, S. Botton, G. A. Pignot-paintrand et al., Seeing structures and measuring properties with transmission electron microscopy images: a simple combination to study size effects in nanoparticle systems, Appl. Phys. Lett, vol.12, p.000267697300053, 2008.

K. Ishizuka and B. Allman, Phase measurement of atomic resolution image using transport of intensity equation, J. Electron Microsc, vol.54, pp.191-197, 2005.

M. Karuppasamy, F. K. Nejadasl, M. Vulovic, A. J. Koster, and R. B. Ravelli, Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate, J. Synchrotron Radiat, vol.18, 2011.

C. T. Koch, Towards full-resolution inline electron holography, Micron, vol.63, pp.69-75, 2014.

P. J. Leibowitz and M. Schaechter, The Attachment of the Bacterial Chromosome to the Cell Membrane, Int. Rev. Cytol, vol.41, issue.08, p.60964, 1975.

A. C. Liu, D. M. Paganin, L. Bourgeois, and P. N. Nakashima, Projected thickness reconstruction from a single defocused transmission electron microscope image of an amorphous object, Ultramicroscopy, vol.111, pp.959-968, 2011.

C. Messaoudi, T. Boudier, C. O. Sorzano, and S. Marco, TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy, BMC Bioinform, vol.8, 2007.

C. Messaoudi, , 2011.

M. Mitome, K. Ishizuka, and Y. Bando, Quantitativeness of phase measurement by transport of intensity equation, J. Electron Microsc, vol.59, pp.33-41, 2010.

M. A. O'keefe, C. J. Hetherington, Y. C. Wang, E. C. Nelson, J. H. Turner et al., Micron, vol.121, pp.90-98, 2019.

C. Malm, J. O. Mueller, R. Ringnalda, J. Pan, M. Thust et al., Sub-?ngstrom high-resolution transmission electron microscopy at 300 keV, Ultramicroscopy, vol.89, pp.215-241, 2001.

D. Paganin and K. A. Nugent, Noninterferometric phase imaging with partially coherent light, Phys. Rev. Lett, vol.80, pp.2586-2589, 1998.

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, pp.33-40, 2002.

R. Popescu, E. Müller, M. Wanner, D. Gerthsen, M. Schowalter et al., Increase of the mean inner Coulomb potential in Au clusters induced by surface tension and its implication for electron scattering, Phys. Rev. B, vol.76, p.235411, 2007.

L. Reimer, Transmission Electron Microscopy -Physics of Image Formation and Microanalysis, 1989.

P. Schiske, Image reconstruction by means of focus series, J. Microsc, vol.207, 2002.

C. A. Schneider, W. S. Rasband, and K. W. Eliceiri, NIH image to ImageJ: 25 years of image analysis, Nat. Methods, vol.9, p.671, 2012.

P. Thevenaz, U. E. Ruttimann, and M. Unser, A pyramid approach to subpixel registration based on intensity, IEEE Trans. Image Process, vol.7, pp.27-41, 1998.

A. Trémeau, R. Schettini, and S. Tominaga, Computational Color Imaging, 2009.

S. Trépout, A. M. Tassin, S. Marco, and P. Bastin, STEM tomography analysis of the trypanosome transition zone, J. Struct. Biol, vol.202, pp.51-60, 2018.

Q. Tseng, URL: https:// sites.google.com/site/qingzongtseng/template-matching-ij-plugin (Online; accessed 27, ImageJ Plugins, vol.11, 2018.

D. Van-dyck, H. Lichte, and K. D. Van-der-mast, Sub-ångström structure characterisation: the Brite-Euram route towards one ångström, Ultramicroscopy, vol.64, pp.1-15, 1996.

A. Verguet, SPCI Plugin Distribution, 2018.

P. Wendykier and J. G. Nagy, Parallel colt: a high-performance Java library for scientific computing and image processing, ACM Trans. Math. Software, vol.37, pp.1-22, 2010.

V. Amandine, Micron, vol.121, pp.90-98, 2019.