Abstract

A crucial issue in the development of therapies to treat pathologies of the central nervous system is represented by the availability of non-invasive methods to study the three-dimensional morphology of spinal cord, with a resolution able to characterize its complex vascular and neuronal organization. X-ray phase contrast micro-tomography enables a high-quality, 3D visualization of both the vascular and neuronal network simultaneously without the need of contrast agents, destructive sample preparations or sectioning. Until now, high resolution investigations of the post-mortem spinal cord in murine models have mostly been performed in spinal cords removed from the spinal canal. We present here post-mortem phase contrast micro-tomography images reconstructed using advanced computational tools to obtain high-resolution and high-contrast 3D images of the fixed spinal cord without removing the bones and preserving the richness of micro-details available when measuring exposed spinal cords. We believe that it represents a significant step toward the in-vivo application.

© 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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  1. N. Hasnan, “International Perspectives on Spinal Cord Injury,” (2013).
  2. M. Soubeyrand, A. Badner, R. Vawda, Y. S. Chung, and M. G. Fehlings, “Very high resolution ultrasound imaging for real-time quantitative visualization of vascular disruption after spinal cord injury,” J. Neurotrauma 31(21), 1767–1775 (2014).
    [Crossref]
  3. M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
    [Crossref]
  4. A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
    [Crossref]
  5. G. J. Cowin, T. J. Butler, N. D. Kurniawan, C. Watson, and R. H. Wallace, “Magnetic resonance microimaging of the spinal cord in the SOD1 mouse model of amyotrophic lateral sclerosis detects motor nerve root degeneration,” NeuroImage 58(1), 69–74 (2011).
    [Crossref]
  6. P. Glover and S. P. Mansfield, “Limits to magnetic resonance microscopy,” Rep. Prog. Phys. 65(10), 1489–1511 (2002).
    [Crossref]
  7. J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
    [Crossref]
  8. C. L. Gregg, A. K. Recknagel, and J. T. Butcher, “Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis,” Methods Mol. Biol. 1189, 47–61 (2015).
    [Crossref]
  9. M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
    [Crossref]
  10. R. Mizutani and Y. Suzuki, “X-ray microtomography in biology,” Micron 43(2-3), 104–115 (2012).
    [Crossref]
  11. P. L. Salmon and A. Y. Sasov, “Application of Nano-CT and High-Resolution Micro-CT to Study Bone Quality and Ultrastructure, Scaffold Biomaterials and Vascular Networks,” 323–331 (2007).
  12. D. P. Clark and C. T. Badea, “Micro-CT of rodents: state-of-the-art and future perspectives,” Phys. Medica 30(6), 619–634 (2014).
    [Crossref]
  13. R. Müller, “Hierarchical microimaging of bone structure and function,” Nat. Rev. Rheumatol. 5(7), 373–381 (2009).
    [Crossref]
  14. B. D. Metscher, “MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues,” BMC Physiol. 9(1), 11 (2009).
    [Crossref]
  15. J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
    [Crossref]
  16. S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
    [Crossref]
  17. J. Hu, Y. Cao, T. Wu, D. Li, and H. Lu, “High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT,” Med. Phys. 41(10), 101904 (2014).
    [Crossref]
  18. D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
    [Crossref]
  19. A. Snigirev, I. Snigireva, V. Kohn, S. Kuznetsov, and I. Schelokov, “On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation,” Rev. Sci. Instrum. 66(12), 5486–5492 (1995).
    [Crossref]
  20. S. W. Wilkins, T. E. Gureyev, D. Gao, A. Pogany, and A. W. Stevenson, “Phase-contrast imaging using polychromatic hard X-rays,” Nature 384(6607), 335–338 (1996).
    [Crossref]
  21. A. Momose, T. Takeda, Y. Itai, and K. Hirano, “Phase-contrast X-ray computed tomography for observing biological soft tissues,” Nat. Med. 2(4), 473–475 (1996).
    [Crossref]
  22. C. David, B. Nöhammer, H. H. Solak, and E. Ziegler, “Differential x-ray phase contrast imaging using a shearing interferometer,” Appl. Phys. Lett. 81(17), 3287–3289 (2002).
    [Crossref]
  23. A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
    [Crossref]
  24. D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
    [Crossref]
  25. M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
    [Crossref]
  26. I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
    [Crossref]
  27. N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
    [Crossref]
  28. Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
    [Crossref]
  29. 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. 206(1), 33–40 (2002).
    [Crossref]
  30. M. A. Beltran, D. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express 18(7), 6423–6436 (2010).
    [Crossref]
  31. M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
    [Crossref]
  32. M. Ullherr and S. Zabler, “Correcting multi material artifacts from single material phase retrieved holo-tomograms with a simple 3D Fourier method,” Opt. Express 23(25), 32718–32727 (2015).
    [Crossref]
  33. L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
    [Crossref]
  34. P. Gilbert, “Iterative methods for the three-dimensional reconstruction of an object from projections,” J. Theor. Biol. 36(1), 105–117 (1972).
    [Crossref]
  35. A. C. Kak, M. Slaney, and G. Wang, Principles of Computerized Tomographic Imaging (1988).
  36. A. Chambolle, V. Caselles, M. Novaga, D. Cremers, and T. Pock, “An introduction to Total Variation for Image Analysis,” 9, 263–340 (2009).
  37. V. V. Estrela, H. A. Magalhães, and O. Saotome, “Total Variation Applications in Computer Vision,” arXiv Prepr. arXiv1603.09599 543–570 (2016).
  38. A. Buzmakov, D. Nikolaev, M. Chukalina, and G. Schaefer, “Efficient and effective regularised ART for computed tomography,” in 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (2011), Vol. 2011, pp. 6200–6203.
  39. M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
    [Crossref]
  40. J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
    [Crossref]
  41. A. V. Bronnikov, “Reconstruction formulas in phase-contrast tomography,” Opt. Commun. 171(4-6), 239–244 (1999).
    [Crossref]
  42. L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
    [Crossref]
  43. D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
    [Crossref]
  44. J. Gregor and T. Benson, “Computational Analysis and Improvement of SIRT,” IEEE Trans. Med. Imaging 27(7), 918–924 (2008).
    [Crossref]
  45. G. Zang, M. Aly, R. Idoughi, P. Wonka, and W. Heidrich, “Super-Resolution and Sparse View CT Reconstruction,” in Proceedings of the European Conference on Computer Vision (ECCV) (2018), pp. 145–161.
  46. A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
    [Crossref]
  47. M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
    [Crossref]
  48. P. C. Hansen and J. H. Jørgensen, “Total Variation and Tomographic Imaging from Projections,” 36th Conf. Dutch-Flemish Numer. Anal. Communities Woudschouten (2011).
  49. E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
    [Crossref]
  50. A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: from pre-clinical applications towards clinics,” Phys. Med. Biol. 58(1), R1–R35 (2013).
    [Crossref]
  51. A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
    [Crossref]
  52. X. Wu, H. Liu, and A. Yan, “X-ray phase-attenuation duality and phase retrieval,” Opt. Lett. 30(4), 379–381 (2005).
    [Crossref]
  53. J. Nocedal and S. J. Wright, Numerical Optimization (Springer Series in Operations Research and Financial Engineering) (Springer, 2000).
  54. F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
    [Crossref]
  55. L. Massimi, F. Brun, M. Fratini, I. Bukreeva, and A. Cedola, “An improved ring removal procedure for in-line x-ray phase contrast tomography,” Phys. Med. Biol. 63(4), 045007 (2018).
    [Crossref]
  56. W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
    [Crossref]

2019 (1)

M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
[Crossref]

2018 (4)

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

L. Massimi, F. Brun, M. Fratini, I. Bukreeva, and A. Cedola, “An improved ring removal procedure for in-line x-ray phase contrast tomography,” Phys. Med. Biol. 63(4), 045007 (2018).
[Crossref]

2017 (4)

A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
[Crossref]

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

2016 (3)

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

2015 (6)

C. L. Gregg, A. K. Recknagel, and J. T. Butcher, “Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis,” Methods Mol. Biol. 1189, 47–61 (2015).
[Crossref]

J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
[Crossref]

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

M. Ullherr and S. Zabler, “Correcting multi material artifacts from single material phase retrieved holo-tomograms with a simple 3D Fourier method,” Opt. Express 23(25), 32718–32727 (2015).
[Crossref]

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

2014 (4)

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

D. P. Clark and C. T. Badea, “Micro-CT of rodents: state-of-the-art and future perspectives,” Phys. Medica 30(6), 619–634 (2014).
[Crossref]

J. Hu, Y. Cao, T. Wu, D. Li, and H. Lu, “High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT,” Med. Phys. 41(10), 101904 (2014).
[Crossref]

M. Soubeyrand, A. Badner, R. Vawda, Y. S. Chung, and M. G. Fehlings, “Very high resolution ultrasound imaging for real-time quantitative visualization of vascular disruption after spinal cord injury,” J. Neurotrauma 31(21), 1767–1775 (2014).
[Crossref]

2013 (2)

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: from pre-clinical applications towards clinics,” Phys. Med. Biol. 58(1), R1–R35 (2013).
[Crossref]

2012 (4)

M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
[Crossref]

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

R. Mizutani and Y. Suzuki, “X-ray microtomography in biology,” Micron 43(2-3), 104–115 (2012).
[Crossref]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

2011 (2)

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

G. J. Cowin, T. J. Butler, N. D. Kurniawan, C. Watson, and R. H. Wallace, “Magnetic resonance microimaging of the spinal cord in the SOD1 mouse model of amyotrophic lateral sclerosis detects motor nerve root degeneration,” NeuroImage 58(1), 69–74 (2011).
[Crossref]

2010 (1)

2009 (3)

D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
[Crossref]

R. Müller, “Hierarchical microimaging of bone structure and function,” Nat. Rev. Rheumatol. 5(7), 373–381 (2009).
[Crossref]

B. D. Metscher, “MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues,” BMC Physiol. 9(1), 11 (2009).
[Crossref]

2008 (2)

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

J. Gregor and T. Benson, “Computational Analysis and Improvement of SIRT,” IEEE Trans. Med. Imaging 27(7), 918–924 (2008).
[Crossref]

2005 (1)

2002 (3)

C. David, B. Nöhammer, H. H. Solak, and E. Ziegler, “Differential x-ray phase contrast imaging using a shearing interferometer,” Appl. Phys. Lett. 81(17), 3287–3289 (2002).
[Crossref]

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. 206(1), 33–40 (2002).
[Crossref]

P. Glover and S. P. Mansfield, “Limits to magnetic resonance microscopy,” Rep. Prog. Phys. 65(10), 1489–1511 (2002).
[Crossref]

2001 (1)

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

1999 (1)

A. V. Bronnikov, “Reconstruction formulas in phase-contrast tomography,” Opt. Commun. 171(4-6), 239–244 (1999).
[Crossref]

1997 (1)

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

1996 (2)

S. W. Wilkins, T. E. Gureyev, D. Gao, A. Pogany, and A. W. Stevenson, “Phase-contrast imaging using polychromatic hard X-rays,” Nature 384(6607), 335–338 (1996).
[Crossref]

A. Momose, T. Takeda, Y. Itai, and K. Hirano, “Phase-contrast X-ray computed tomography for observing biological soft tissues,” Nat. Med. 2(4), 473–475 (1996).
[Crossref]

1995 (1)

A. Snigirev, I. Snigireva, V. Kohn, S. Kuznetsov, and I. Schelokov, “On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation,” Rev. Sci. Instrum. 66(12), 5486–5492 (1995).
[Crossref]

1972 (1)

P. Gilbert, “Iterative methods for the three-dimensional reconstruction of an object from projections,” J. Theor. Biol. 36(1), 105–117 (1972).
[Crossref]

Accardo, A.

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

Alejandre-Lafont, E.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Altantzis, T.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

Althöhn, U.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Aly, M.

G. Zang, M. Aly, R. Idoughi, P. Wonka, and W. Heidrich, “Super-Resolution and Sparse View CT Reconstruction,” in Proceedings of the European Conference on Computer Vision (ECCV) (2018), pp. 145–161.

Andres-Thio, N.

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

Annapragada, A. V.

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

Arfelli, F.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Arganda-Carreras, I.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Asadchikov, V. E.

M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
[Crossref]

Badea, C. T.

D. P. Clark and C. T. Badea, “Micro-CT of rodents: state-of-the-art and future perspectives,” Phys. Medica 30(6), 619–634 (2014).
[Crossref]

Badner, A.

M. Soubeyrand, A. Badner, R. Vawda, Y. S. Chung, and M. G. Fehlings, “Very high resolution ultrasound imaging for real-time quantitative visualization of vascular disruption after spinal cord injury,” J. Neurotrauma 31(21), 1767–1775 (2014).
[Crossref]

Baldacci, F.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Bals, S.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

Batenburg, K. J.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

Battaglia, G.

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Becker, K.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Beltran, M.

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

Beltran, M. A.

Benson, T.

J. Gregor and T. Benson, “Computational Analysis and Improvement of SIRT,” IEEE Trans. Med. Imaging 27(7), 918–924 (2008).
[Crossref]

Benveniste, H.

D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
[Crossref]

Bernstein, I. M.

M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
[Crossref]

Bidola, P.

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

Billé, F.

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

Bleichrodt, F.

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

Bradke, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Bravin, A.

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: from pre-clinical applications towards clinics,” Phys. Med. Biol. 58(1), R1–R35 (2013).
[Crossref]

Broche, L.

A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
[Crossref]

Bronnikov, A. V.

A. V. Bronnikov, “Reconstruction formulas in phase-contrast tomography,” Opt. Commun. 171(4-6), 239–244 (1999).
[Crossref]

Brun, E.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Brun, F.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

L. Massimi, F. Brun, M. Fratini, I. Bukreeva, and A. Cedola, “An improved ring removal procedure for in-line x-ray phase contrast tomography,” Phys. Med. Biol. 63(4), 045007 (2018).
[Crossref]

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Bucci, D.

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Buckley, G. A.

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

Bukreeva, I.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

L. Massimi, F. Brun, M. Fratini, I. Bukreeva, and A. Cedola, “An improved ring removal procedure for in-line x-ray phase contrast tomography,” Phys. Med. Biol. 63(4), 045007 (2018).
[Crossref]

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Butcher, J. T.

C. L. Gregg, A. K. Recknagel, and J. T. Butcher, “Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis,” Methods Mol. Biol. 1189, 47–61 (2015).
[Crossref]

Butler, T. J.

G. J. Cowin, T. J. Butler, N. D. Kurniawan, C. Watson, and R. H. Wallace, “Magnetic resonance microimaging of the spinal cord in the SOD1 mouse model of amyotrophic lateral sclerosis detects motor nerve root degeneration,” NeuroImage 58(1), 69–74 (2011).
[Crossref]

Buzmakov, A.

A. Buzmakov, D. Nikolaev, M. Chukalina, and G. Schaefer, “Efficient and effective regularised ART for computed tomography,” in 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (2011), Vol. 2011, pp. 6200–6203.

Buzmakov, A. V.

M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
[Crossref]

Campi, G.

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Cantatore, G.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Cao, Y.

J. Hu, Y. Cao, T. Wu, D. Li, and H. Lu, “High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT,” Med. Phys. 41(10), 101904 (2014).
[Crossref]

Cardona, A.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Cardoso, M. B.

J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
[Crossref]

Caselles, V.

A. Chambolle, V. Caselles, M. Novaga, D. Cremers, and T. Pock, “An introduction to Total Variation for Image Analysis,” 9, 263–340 (2009).

Castelli, E.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Cedola, A.

L. Massimi, F. Brun, M. Fratini, I. Bukreeva, and A. Cedola, “An improved ring removal procedure for in-line x-ray phase contrast tomography,” Phys. Med. Biol. 63(4), 045007 (2018).
[Crossref]

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Chambolle, A.

A. Chambolle, V. Caselles, M. Novaga, D. Cremers, and T. Pock, “An introduction to Total Variation for Image Analysis,” 9, 263–340 (2009).

Chapman, D.

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Chen, D.

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

Chukalina, M.

A. Buzmakov, D. Nikolaev, M. Chukalina, and G. Schaefer, “Efficient and effective regularised ART for computed tomography,” in 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (2011), Vol. 2011, pp. 6200–6203.

Chukalina, M. V.

M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
[Crossref]

Chung, Y. S.

M. Soubeyrand, A. Badner, R. Vawda, Y. S. Chung, and M. G. Fehlings, “Very high resolution ultrasound imaging for real-time quantitative visualization of vascular disruption after spinal cord injury,” J. Neurotrauma 31(21), 1767–1775 (2014).
[Crossref]

Clark, D. P.

D. P. Clark and C. T. Badea, “Micro-CT of rodents: state-of-the-art and future perspectives,” Phys. Medica 30(6), 619–634 (2014).
[Crossref]

Cleland, T. A.

M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
[Crossref]

Coan, P.

A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
[Crossref]

A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: from pre-clinical applications towards clinics,” Phys. Med. Biol. 58(1), R1–R35 (2013).
[Crossref]

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Connor, D. M.

D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
[Crossref]

Cowin, G. J.

G. J. Cowin, T. J. Butler, N. D. Kurniawan, C. Watson, and R. H. Wallace, “Magnetic resonance microimaging of the spinal cord in the SOD1 mouse model of amyotrophic lateral sclerosis detects motor nerve root degeneration,” NeuroImage 58(1), 69–74 (2011).
[Crossref]

Cremers, D.

A. Chambolle, V. Caselles, M. Novaga, D. Cremers, and T. Pock, “An introduction to Total Variation for Image Analysis,” 9, 263–340 (2009).

Crossley, K. J.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

Croton, L. C. P.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

Das, N. M.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

David, C.

C. David, B. Nöhammer, H. H. Solak, and E. Ziegler, “Differential x-ray phase contrast imaging using a shearing interferometer,” Appl. Phys. Lett. 81(17), 3287–3289 (2002).
[Crossref]

De Beenhouwer, J.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

de S. e Silva, J. M.

J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
[Crossref]

Delaire, F.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Dierolf, M.

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

Dilmanian, F. A.

D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
[Crossref]

Dodt, H. U.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Dreossi, D.

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

Dudak, J.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Economides, A.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Eliceiri, K.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Ertürk, A.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Estrela, V. V.

V. V. Estrela, H. A. Magalhães, and O. Saotome, “Total Variation Applications in Computer Vision,” arXiv Prepr. arXiv1603.09599 543–570 (2016).

Farrar, M. J.

M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
[Crossref]

Fehlings, M. G.

M. Soubeyrand, A. Badner, R. Vawda, Y. S. Chung, and M. G. Fehlings, “Very high resolution ultrasound imaging for real-time quantitative visualization of vascular disruption after spinal cord injury,” J. Neurotrauma 31(21), 1767–1775 (2014).
[Crossref]

Ferrero, C.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Fetcho, J. R.

M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
[Crossref]

Förstner, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Fouras, A.

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

Fratini, M.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

L. Massimi, F. Brun, M. Fratini, I. Bukreeva, and A. Cedola, “An improved ring removal procedure for in-line x-ray phase contrast tomography,” Phys. Med. Biol. 63(4), 045007 (2018).
[Crossref]

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Freud, N.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Friedrich, H.

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

Frise, E.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Gao, D.

S. W. Wilkins, T. E. Gureyev, D. Gao, A. Pogany, and A. W. Stevenson, “Phase-contrast imaging using polychromatic hard X-rays,” Nature 384(6607), 335–338 (1996).
[Crossref]

Gasilov, S.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Gassmann, M.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Ghaghada, K. B.

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

Gilbert, P.

P. Gilbert, “Iterative methods for the three-dimensional reconstruction of an object from projections,” J. Theor. Biol. 36(1), 105–117 (1972).
[Crossref]

Giove, F.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Glover, P.

P. Glover and S. P. Mansfield, “Limits to magnetic resonance microscopy,” Rep. Prog. Phys. 65(10), 1489–1511 (2002).
[Crossref]

Gmür, N.

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Goris, B.

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

Gradl, R.

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

Gregg, C. L.

C. L. Gregg, A. K. Recknagel, and J. T. Butcher, “Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis,” Methods Mol. Biol. 1189, 47–61 (2015).
[Crossref]

Gregor, J.

J. Gregor and T. Benson, “Computational Analysis and Improvement of SIRT,” IEEE Trans. Med. Imaging 27(7), 918–924 (2008).
[Crossref]

Gröhn, O.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

Gureyev, T. E.

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

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. 206(1), 33–40 (2002).
[Crossref]

S. W. Wilkins, T. E. Gureyev, D. Gao, A. Pogany, and A. W. Stevenson, “Phase-contrast imaging using polychromatic hard X-rays,” Nature 384(6607), 335–338 (1996).
[Crossref]

Hansen, P. C.

P. C. Hansen and J. H. Jørgensen, “Total Variation and Tomographic Imaging from Projections,” 36th Conf. Dutch-Flemish Numer. Anal. Communities Woudschouten (2011).

Hartenstein, V.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Hasnan, N.

N. Hasnan, “International Perspectives on Spinal Cord Injury,” (2013).

Hatsell, S.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Hehn, L.

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

Heidrich, W.

G. Zang, M. Aly, R. Idoughi, P. Wonka, and W. Heidrich, “Super-Resolution and Sparse View CT Reconstruction,” in Proceedings of the European Conference on Computer Vision (ECCV) (2018), pp. 145–161.

Heinzer, S.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Hellal, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Hermanova, Z.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Hirano, K.

A. Momose, T. Takeda, Y. Itai, and K. Hirano, “Phase-contrast X-ray computed tomography for observing biological soft tissues,” Nat. Med. 2(4), 473–475 (1996).
[Crossref]

Hooper, S.

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

Hooper, S. B.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

Hu, J.

J. Hu, Y. Cao, T. Wu, D. Li, and H. Lu, “High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT,” Med. Phys. 41(10), 101904 (2014).
[Crossref]

Huang, L.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Hübener, M.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Idone, V.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Idoughi, R.

G. Zang, M. Aly, R. Idoughi, P. Wonka, and W. Heidrich, “Super-Resolution and Sparse View CT Reconstruction,” in Proceedings of the European Conference on Computer Vision (ECCV) (2018), pp. 145–161.

Ingacheva, A. S.

M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
[Crossref]

Itai, Y.

A. Momose, T. Takeda, Y. Itai, and K. Hirano, “Phase-contrast X-ray computed tomography for observing biological soft tissues,” Nat. Med. 2(4), 473–475 (1996).
[Crossref]

Jährling, N.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Jarnias, C.

A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
[Crossref]

Johnston, R. E.

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Jørgensen, J. H.

P. C. Hansen and J. H. Jørgensen, “Total Variation and Tomographic Imaging from Projections,” 36th Conf. Dutch-Flemish Numer. Anal. Communities Woudschouten (2011).

Kak, A. C.

A. C. Kak, M. Slaney, and G. Wang, Principles of Computerized Tomographic Imaging (1988).

Kampschulte, M.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Karch, J.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Kaynig, V.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Keck, T.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Kerr, L. T.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

Kimm, M. A.

J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
[Crossref]

Kirchhoff, F.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Kitchen, M.

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

Kitchen, M. J.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

M. A. Beltran, D. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express 18(7), 6423–6436 (2010).
[Crossref]

Kohn, V.

A. Snigirev, I. Snigireva, V. Kohn, S. Kuznetsov, and I. Schelokov, “On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation,” Rev. Sci. Instrum. 66(12), 5486–5492 (1995).
[Crossref]

Kramer, E.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Krejci, F.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Kritzer, M. F.

D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
[Crossref]

Krivonosov, Y. S.

M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
[Crossref]

Krombach, G. A.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Krucker, T.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Kuhn, G.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Kurniawan, N. D.

G. J. Cowin, T. J. Butler, N. D. Kurniawan, C. Watson, and R. H. Wallace, “Magnetic resonance microimaging of the spinal cord in the SOD1 mouse model of amyotrophic lateral sclerosis detects motor nerve root degeneration,” NeuroImage 58(1), 69–74 (2011).
[Crossref]

Kuznetsov, S.

A. Snigirev, I. Snigireva, V. Kohn, S. Kuznetsov, and I. Schelokov, “On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation,” Rev. Sci. Instrum. 66(12), 5486–5492 (1995).
[Crossref]

Kvacek, J.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Langheinirch, A. C.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Létang, J. M.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Li, D.

J. Hu, Y. Cao, T. Wu, D. Li, and H. Lu, “High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT,” Med. Phys. 41(10), 101904 (2014).
[Crossref]

Litzlbauer, H. D.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Liu, H.

Longair, M.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Longo, R.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Lu, H.

J. Hu, Y. Cao, T. Wu, D. Li, and H. Lu, “High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT,” Med. Phys. 41(10), 101904 (2014).
[Crossref]

Magalhães, H. A.

V. V. Estrela, H. A. Magalhães, and O. Saotome, “Total Variation Applications in Computer Vision,” arXiv Prepr. arXiv1603.09599 543–570 (2016).

Manakov, I.

A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
[Crossref]

Mansfield, S. P.

P. Glover and S. P. Mansfield, “Limits to magnetic resonance microscopy,” Rep. Prog. Phys. 65(10), 1489–1511 (2002).
[Crossref]

Martels, G.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Marti, H. H.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Massimi, L.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

L. Massimi, F. Brun, M. Fratini, I. Bukreeva, and A. Cedola, “An improved ring removal procedure for in-line x-ray phase contrast tomography,” Phys. Med. Biol. 63(4), 045007 (2018).
[Crossref]

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

Mastrogiacomo, M.

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Mauch, C. P.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Maugeri, L.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

Mayo, S. C.

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. 206(1), 33–40 (2002).
[Crossref]

Meganck, J. A.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Menk, R.

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Menk, R. H.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Metscher, B. D.

B. D. Metscher, “MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues,” BMC Physiol. 9(1), 11 (2009).
[Crossref]

Meyer, E. P.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Mezerji, H. H.

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

Milewicz, D. M.

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

Miller, L. M.

D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
[Crossref]

Miller, P. R.

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. 206(1), 33–40 (2002).
[Crossref]

Miller, S. L.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

Miocchi, P.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

Mittone, A.

A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
[Crossref]

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Mizutani, R.

R. Mizutani and Y. Suzuki, “X-ray microtomography in biology,” Micron 43(2-3), 104–115 (2012).
[Crossref]

Modregger, P.

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Momose, A.

A. Momose, T. Takeda, Y. Itai, and K. Hirano, “Phase-contrast X-ray computed tomography for observing biological soft tissues,” Nat. Med. 2(4), 473–475 (1996).
[Crossref]

Morgan, K.

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

Morgan, K. S.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

Mrzilkova, J.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Müller, R.

R. Müller, “Hierarchical microimaging of bone structure and function,” Nat. Rev. Rheumatol. 5(7), 373–381 (2009).
[Crossref]

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Murphy, A.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Nannuru, K.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Nikolaev, D.

A. Buzmakov, D. Nikolaev, M. Chukalina, and G. Schaefer, “Efficient and effective regularised ART for computed tomography,” in 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (2011), Vol. 2011, pp. 6200–6203.

Nikolaev, D. P.

M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
[Crossref]

Nocedal, J.

J. Nocedal and S. J. Wright, Numerical Optimization (Springer Series in Operations Research and Financial Engineering) (Springer, 2000).

Noël, P. B.

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
[Crossref]

Nöhammer, B.

C. David, B. Nöhammer, H. H. Solak, and E. Ziegler, “Differential x-ray phase contrast imaging using a shearing interferometer,” Appl. Phys. Lett. 81(17), 3287–3289 (2002).
[Crossref]

Noichl, W.

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

Novaga, M.

A. Chambolle, V. Caselles, M. Novaga, D. Cremers, and T. Pock, “An introduction to Total Variation for Image Analysis,” 9, 263–340 (2009).

Nurmi, A.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

Olivo, A.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Paganin, D.

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

M. A. Beltran, D. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express 18(7), 6423–6436 (2010).
[Crossref]

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. 206(1), 33–40 (2002).
[Crossref]

Paganin, D. M.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

Paldino, M. J.

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

Palenstijn, W. J.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

Pani, S.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Patzelt, M.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Pfeiffer, F.

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
[Crossref]

Pietzsch, T.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Pisano, E.

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Pock, T.

A. Chambolle, V. Caselles, M. Novaga, D. Cremers, and T. Pock, “An introduction to Total Variation for Image Analysis,” 9, 263–340 (2009).

Pogany, A.

S. W. Wilkins, T. E. Gureyev, D. Gao, A. Pogany, and A. W. Stevenson, “Phase-contrast imaging using polychromatic hard X-rays,” Nature 384(6607), 335–338 (1996).
[Crossref]

Poropat, P.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Preibisch, S.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Prest, M.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Provinciali, G. B.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

Pugliese, R.

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

Recknagel, A. K.

C. L. Gregg, A. K. Recknagel, and J. T. Butcher, “Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis,” Methods Mol. Biol. 1189, 47–61 (2015).
[Crossref]

Rendon, D.

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

Requardt, H.

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Reser, D.

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

Richter, M.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Rigon, L.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Rueden, C. T.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Saalfeld, S.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Salmon, P. L.

P. L. Salmon and A. Y. Sasov, “Application of Nano-CT and High-Resolution Micro-CT to Study Bone Quality and Ultrastructure, Scaffold Biomaterials and Vascular Networks,” 323–331 (2007).

Saotome, O.

V. V. Estrela, H. A. Magalhães, and O. Saotome, “Total Variation Applications in Computer Vision,” arXiv Prepr. arXiv1603.09599 543–570 (2016).

Sarrut, D.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Sasov, A. Y.

P. L. Salmon and A. Y. Sasov, “Application of Nano-CT and High-Resolution Micro-CT to Study Bone Quality and Ultrastructure, Scaffold Biomaterials and Vascular Networks,” 323–331 (2007).

Sayers, D.

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Schaefer, G.

A. Buzmakov, D. Nikolaev, M. Chukalina, and G. Schaefer, “Efficient and effective regularised ART for computed tomography,” in 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (2011), Vol. 2011, pp. 6200–6203.

Schaffer, C. B.

M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
[Crossref]

Schelokov, I.

A. Snigirev, I. Snigireva, V. Kohn, S. Kuznetsov, and I. Schelokov, “On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation,” Rev. Sci. Instrum. 66(12), 5486–5492 (1995).
[Crossref]

Schindelin, J.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Schlafer, D. H.

M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
[Crossref]

Schmid, B.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Schwab, J. D.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Sender, J.

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Sierra, A.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

Sijbers, J.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

Siu, K.

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

Slaney, M.

A. C. Kak, M. Slaney, and G. Wang, Principles of Computerized Tomographic Imaging (1988).

Smekens, F.

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

Snigirev, A.

A. Snigirev, I. Snigireva, V. Kohn, S. Kuznetsov, and I. Schelokov, “On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation,” Rev. Sci. Instrum. 66(12), 5486–5492 (1995).
[Crossref]

Snigireva, I.

A. Snigirev, I. Snigireva, V. Kohn, S. Kuznetsov, and I. Schelokov, “On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation,” Rev. Sci. Instrum. 66(12), 5486–5492 (1995).
[Crossref]

Solak, H. H.

C. David, B. Nöhammer, H. H. Solak, and E. Ziegler, “Differential x-ray phase contrast imaging using a shearing interferometer,” Appl. Phys. Lett. 81(17), 3287–3289 (2002).
[Crossref]

Soubeyrand, M.

M. Soubeyrand, A. Badner, R. Vawda, Y. S. Chung, and M. G. Fehlings, “Very high resolution ultrasound imaging for real-time quantitative visualization of vascular disruption after spinal cord injury,” J. Neurotrauma 31(21), 1767–1775 (2014).
[Crossref]

Spanò, R.

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

Stampanoni, M.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Starosolski, Z.

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

Stefanutti, E.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

Steffens, H.

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

Stevenson, A. W.

S. W. Wilkins, T. E. Gureyev, D. Gao, A. Pogany, and A. W. Stevenson, “Phase-contrast imaging using polychromatic hard X-rays,” Nature 384(6607), 335–338 (1996).
[Crossref]

Suortti, P.

A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: from pre-clinical applications towards clinics,” Phys. Med. Biol. 58(1), R1–R35 (2013).
[Crossref]

Suzuki, Y.

R. Mizutani and Y. Suzuki, “X-ray microtomography in biology,” Micron 43(2-3), 104–115 (2012).
[Crossref]

Takeda, T.

A. Momose, T. Takeda, Y. Itai, and K. Hirano, “Phase-contrast X-ray computed tomography for observing biological soft tissues,” Nat. Med. 2(4), 473–475 (1996).
[Crossref]

Thomlinson, W.

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Tinevez, J.-Y.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Tomancak, P.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Tromba, G.

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

Uccelli, A.

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

Uesugi, K.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

M. A. Beltran, D. Paganin, K. Uesugi, and M. J. Kitchen, “2D and 3D X-ray phase retrieval of multi-material objects using a single defocus distance,” Opt. Express 18(7), 6423–6436 (2010).
[Crossref]

Ullherr, M.

Ulmann-Schuler, A.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Vallazza, E.

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

van Aarle, W.

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

Vawda, R.

M. Soubeyrand, A. Badner, R. Vawda, Y. S. Chung, and M. G. Fehlings, “Very high resolution ultrasound imaging for real-time quantitative visualization of vascular disruption after spinal cord injury,” J. Neurotrauma 31(21), 1767–1775 (2014).
[Crossref]

Venturi, C.

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

Villamizar, C. A.

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

Vogel, J.

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

Wallace, M. J.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

Wallace, R. H.

G. J. Cowin, T. J. Butler, N. D. Kurniawan, C. Watson, and R. H. Wallace, “Magnetic resonance microimaging of the spinal cord in the SOD1 mouse model of amyotrophic lateral sclerosis detects motor nerve root degeneration,” NeuroImage 58(1), 69–74 (2011).
[Crossref]

Wang, G.

A. C. Kak, M. Slaney, and G. Wang, Principles of Computerized Tomographic Imaging (1988).

Wang, L.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Wang, L.-H.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Washburn, D.

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Watson, C.

G. J. Cowin, T. J. Butler, N. D. Kurniawan, C. Watson, and R. H. Wallace, “Magnetic resonance microimaging of the spinal cord in the SOD1 mouse model of amyotrophic lateral sclerosis detects motor nerve root degeneration,” NeuroImage 58(1), 69–74 (2011).
[Crossref]

Wen, X.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

White, D. J.

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Wilkins, S. W.

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. 206(1), 33–40 (2002).
[Crossref]

S. W. Wilkins, T. E. Gureyev, D. Gao, A. Pogany, and A. W. Stevenson, “Phase-contrast imaging using polychromatic hard X-rays,” Nature 384(6607), 335–338 (1996).
[Crossref]

Wonka, P.

G. Zang, M. Aly, R. Idoughi, P. Wonka, and W. Heidrich, “Super-Resolution and Sparse View CT Reconstruction,” in Proceedings of the European Conference on Computer Vision (ECCV) (2018), pp. 145–161.

Wright, S. J.

J. Nocedal and S. J. Wright, Numerical Optimization (Springer Series in Operations Research and Financial Engineering) (Springer, 2000).

Wu, T.

J. Hu, Y. Cao, T. Wu, D. Li, and H. Lu, “High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT,” Med. Phys. 41(10), 101904 (2014).
[Crossref]

Wu, X.

Xie, L.

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Yagi, N.

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

Yan, A.

Zabler, S.

Zach, P.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Zanette, I.

J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
[Crossref]

Zang, G.

G. Zang, M. Aly, R. Idoughi, P. Wonka, and W. Heidrich, “Super-Resolution and Sparse View CT Reconstruction,” in Proceedings of the European Conference on Computer Vision (ECCV) (2018), pp. 145–161.

Zemlicka, J.

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

Zhong, Z.

D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
[Crossref]

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Ziegler, E.

C. David, B. Nöhammer, H. H. Solak, and E. Ziegler, “Differential x-ray phase contrast imaging using a shearing interferometer,” Appl. Phys. Lett. 81(17), 3287–3289 (2002).
[Crossref]

Adv. Struct. Chem. Imaging (1)

F. Brun, L. Massimi, M. Fratini, D. Dreossi, F. Billé, A. Accardo, R. Pugliese, and A. Cedola, “SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows,” Adv. Struct. Chem. Imaging 3(1), 4 (2017).
[Crossref]

APL Bioeng. (1)

L. Hehn, K. Morgan, P. Bidola, W. Noichl, R. Gradl, M. Dierolf, P. B. Noël, and F. Pfeiffer, “Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography,” APL Bioeng. 2(1), 016105 (2018).
[Crossref]

Appl. Phys. Lett. (1)

C. David, B. Nöhammer, H. H. Solak, and E. Ziegler, “Differential x-ray phase contrast imaging using a shearing interferometer,” Appl. Phys. Lett. 81(17), 3287–3289 (2002).
[Crossref]

BMC Physiol. (1)

B. D. Metscher, “MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues,” BMC Physiol. 9(1), 11 (2009).
[Crossref]

Bull. Russ. Acad. Sci.: Phys. (1)

M. V. Chukalina, A. S. Ingacheva, A. V. Buzmakov, Y. S. Krivonosov, V. E. Asadchikov, and D. P. Nikolaev, “A Hardware and Software System for Tomographic Research: Reconstruction via Regularization,” Bull. Russ. Acad. Sci.: Phys. 83(2), 150–154 (2019).
[Crossref]

IEEE Trans. Med. Imaging (1)

J. Gregor and T. Benson, “Computational Analysis and Improvement of SIRT,” IEEE Trans. Med. Imaging 27(7), 918–924 (2008).
[Crossref]

J. Instrum. (1)

E. Stefanutti, A. Sierra, P. Miocchi, L. Massimi, F. Brun, L. Maugeri, I. Bukreeva, A. Nurmi, G. B. Provinciali, G. Tromba, O. Gröhn, F. Giove, A. Cedola, and M. Fratini, “Assessment of the effects of different sample perfusion procedures on phase-contrast tomographic images of mouse spinal cord,” J. Instrum. 13(03), C03027 (2018).
[Crossref]

J. Microsc. (1)

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. 206(1), 33–40 (2002).
[Crossref]

J. Neurotrauma (1)

M. Soubeyrand, A. Badner, R. Vawda, Y. S. Chung, and M. G. Fehlings, “Very high resolution ultrasound imaging for real-time quantitative visualization of vascular disruption after spinal cord injury,” J. Neurotrauma 31(21), 1767–1775 (2014).
[Crossref]

J. Synchrotron Radiat. (2)

A. Mittone, I. Manakov, L. Broche, C. Jarnias, P. Coan, and A. Bravin, “Characterization of a sCMOS-based high-resolution imaging system,” J. Synchrotron Radiat. 24(6), 1226–1236 (2017).
[Crossref]

A. Mittone, F. Baldacci, A. Bravin, E. Brun, F. Delaire, C. Ferrero, S. Gasilov, N. Freud, J. M. Létang, D. Sarrut, F. Smekens, and P. Coan, “An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy,” J. Synchrotron Radiat. 20(5), 785–792 (2013).
[Crossref]

J. Theor. Biol. (1)

P. Gilbert, “Iterative methods for the three-dimensional reconstruction of an object from projections,” J. Theor. Biol. 36(1), 105–117 (1972).
[Crossref]

Med. Phys. (2)

A. Olivo, F. Arfelli, G. Cantatore, R. Longo, R. H. Menk, S. Pani, M. Prest, P. Poropat, L. Rigon, G. Tromba, E. Vallazza, and E. Castelli, “An innovative digital imaging set-up allowing a low-dose approach to phase contrast applications in the medical field,” Med. Phys. 28(8), 1610–1619 (2001).
[Crossref]

J. Hu, Y. Cao, T. Wu, D. Li, and H. Lu, “High-resolution three-dimensional visualization of the rat spinal cord microvasculature by synchrotron radiation micro-CT,” Med. Phys. 41(10), 101904 (2014).
[Crossref]

Methods Mol. Biol. (1)

C. L. Gregg, A. K. Recknagel, and J. T. Butcher, “Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis,” Methods Mol. Biol. 1189, 47–61 (2015).
[Crossref]

Micron (1)

R. Mizutani and Y. Suzuki, “X-ray microtomography in biology,” Micron 43(2-3), 104–115 (2012).
[Crossref]

Nat. Med. (2)

A. Ertürk, C. P. Mauch, F. Hellal, F. Förstner, T. Keck, K. Becker, N. Jährling, H. Steffens, M. Richter, M. Hübener, E. Kramer, F. Kirchhoff, H. U. Dodt, and F. Bradke, “Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury,” Nat. Med. 18(1), 166–171 (2012).
[Crossref]

A. Momose, T. Takeda, Y. Itai, and K. Hirano, “Phase-contrast X-ray computed tomography for observing biological soft tissues,” Nat. Med. 2(4), 473–475 (1996).
[Crossref]

Nat. Methods (2)

M. J. Farrar, I. M. Bernstein, D. H. Schlafer, T. A. Cleland, J. R. Fetcho, and C. B. Schaffer, “Chronic in vivo imaging in the mouse spinal cord using an implanted chamber,” Nat. Methods 9(3), 297–302 (2012).
[Crossref]

J. Schindelin, I. Arganda-Carreras, E. Frise, V. Kaynig, M. Longair, T. Pietzsch, S. Preibisch, C. T. Rueden, S. Saalfeld, B. Schmid, J.-Y. Tinevez, D. J. White, V. Hartenstein, K. Eliceiri, P. Tomancak, and A. Cardona, “Fiji: an open-source platform for biological-image analysis,” Nat. Methods 9(7), 676–682 (2012).
[Crossref]

Nat. Rev. Rheumatol. (1)

R. Müller, “Hierarchical microimaging of bone structure and function,” Nat. Rev. Rheumatol. 5(7), 373–381 (2009).
[Crossref]

Nature (1)

S. W. Wilkins, T. E. Gureyev, D. Gao, A. Pogany, and A. W. Stevenson, “Phase-contrast imaging using polychromatic hard X-rays,” Nature 384(6607), 335–338 (1996).
[Crossref]

NeuroImage (3)

D. M. Connor, H. Benveniste, F. A. Dilmanian, M. F. Kritzer, L. M. Miller, and Z. Zhong, “Computed tomography of amyloid plaques in a mouse model of Alzheimer’s disease using diffraction enhanced imaging,” NeuroImage 46(4), 908–914 (2009).
[Crossref]

S. Heinzer, G. Kuhn, T. Krucker, E. P. Meyer, A. Ulmann-Schuler, M. Stampanoni, M. Gassmann, H. H. Marti, R. Müller, and J. Vogel, “Novel three-dimensional analysis tool for vascular trees indicates complete micro-networks, not single capillaries, as the angiogenic endpoint in mice overexpressing human VEGF(165) in the brain,” NeuroImage 39(4), 1549–1558 (2008).
[Crossref]

G. J. Cowin, T. J. Butler, N. D. Kurniawan, C. Watson, and R. H. Wallace, “Magnetic resonance microimaging of the spinal cord in the SOD1 mouse model of amyotrophic lateral sclerosis detects motor nerve root degeneration,” NeuroImage 58(1), 69–74 (2011).
[Crossref]

Opt. Commun. (1)

A. V. Bronnikov, “Reconstruction formulas in phase-contrast tomography,” Opt. Commun. 171(4-6), 239–244 (1999).
[Crossref]

Opt. Express (2)

Opt. Lett. (1)

Phys. Med. Biol. (4)

M. Beltran, D. Paganin, K. Siu, A. Fouras, S. Hooper, D. Reser, and M. Kitchen, “Interface-specific x-ray phase retrieval tomography of complex biological organs,” Phys. Med. Biol. 56(23), 7353–7369 (2011).
[Crossref]

L. Massimi, F. Brun, M. Fratini, I. Bukreeva, and A. Cedola, “An improved ring removal procedure for in-line x-ray phase contrast tomography,” Phys. Med. Biol. 63(4), 045007 (2018).
[Crossref]

A. Bravin, P. Coan, and P. Suortti, “X-ray phase-contrast imaging: from pre-clinical applications towards clinics,” Phys. Med. Biol. 58(1), R1–R35 (2013).
[Crossref]

D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmür, Z. Zhong, R. Menk, F. Arfelli, and D. Sayers, “Diffraction enhanced x-ray imaging,” Phys. Med. Biol. 42(11), 2015–2025 (1997).
[Crossref]

Phys. Medica (1)

D. P. Clark and C. T. Badea, “Micro-CT of rodents: state-of-the-art and future perspectives,” Phys. Medica 30(6), 619–634 (2014).
[Crossref]

PLoS One (1)

N. M. Das, S. Hatsell, K. Nannuru, L. Huang, X. Wen, L. Wang, L.-H. Wang, V. Idone, J. A. Meganck, A. Murphy, A. Economides, and L. Xie, “In Vivo Quantitative Microcomputed Tomographic Analysis of Vasculature and Organs in a Normal and Diseased Mouse Model,” PLoS One 11(2), e0150085 (2016).
[Crossref]

Rep. Prog. Phys. (1)

P. Glover and S. P. Mansfield, “Limits to magnetic resonance microscopy,” Rep. Prog. Phys. 65(10), 1489–1511 (2002).
[Crossref]

Rev. Sci. Instrum. (1)

A. Snigirev, I. Snigireva, V. Kohn, S. Kuznetsov, and I. Schelokov, “On the possibilities of x-ray phase contrast microimaging by coherent high-energy synchrotron radiation,” Rev. Sci. Instrum. 66(12), 5486–5492 (1995).
[Crossref]

Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren (1)

M. Kampschulte, A. C. Langheinirch, J. Sender, H. D. Litzlbauer, U. Althöhn, J. D. Schwab, E. Alejandre-Lafont, G. Martels, and G. A. Krombach, “Nano-Computed Tomography: Technique and Applications,” Rofo-fortschritte Auf Dem Gebiet Der Rontgenstrahlen Und Der Bildgeb. Verfahren 188(02), 146–154 (2016).
[Crossref]

Sci. Rep. (7)

J. Dudak, J. Zemlicka, J. Karch, M. Patzelt, J. Mrzilkova, P. Zach, Z. Hermanova, J. Kvacek, and F. Krejci, “High-contrast X-ray micro-radiography and micro-CT of ex-vivo soft tissue murine organs utilizing ethanol fixation and large area photon-counting detector,” Sci. Rep. 6(1), 30385 (2016).
[Crossref]

J. M. de S. e Silva, I. Zanette, P. B. Noël, M. B. Cardoso, M. A. Kimm, and F. Pfeiffer, “Three-dimensional non-destructive soft-tissue visualization with X-ray staining micro-tomography,” Sci. Rep. 5(1), 14088 (2015).
[Crossref]

M. Fratini, I. Bukreeva, G. Campi, F. Brun, G. Tromba, P. Modregger, D. Bucci, G. Battaglia, R. Spanò, M. Mastrogiacomo, H. Requardt, F. Giove, A. Bravin, and A. Cedola, “Simultaneous submicrometric 3D imaging of the micro-vascular network and the neuronal system in a mouse spinal cord,” Sci. Rep. 5(1), 8514 (2015).
[Crossref]

I. Bukreeva, G. Campi, M. Fratini, R. Spanò, D. Bucci, G. Battaglia, F. Giove, A. Bravin, A. Uccelli, C. Venturi, M. Mastrogiacomo, and A. Cedola, “Quantitative 3D investigation of Neuronal network in mouse spinal cord model,” Sci. Rep. 7(1), 41054 (2017).
[Crossref]

Z. Starosolski, C. A. Villamizar, D. Rendon, M. J. Paldino, D. M. Milewicz, K. B. Ghaghada, and A. V. Annapragada, “Ultra High-Resolution In vivo Computed Tomography Imaging of Mouse Cerebrovasculature Using a Long Circulating Blood Pool Contrast Agent,” Sci. Rep. 5(1), 10178 (2015).
[Crossref]

L. C. P. Croton, K. S. Morgan, D. M. Paganin, L. T. Kerr, M. J. Wallace, K. J. Crossley, S. L. Miller, N. Yagi, K. Uesugi, S. B. Hooper, and M. J. Kitchen, “In situ phase contrast X-ray brain CT,” Sci. Rep. 8(1), 11412 (2018).
[Crossref]

M. J. Kitchen, G. A. Buckley, T. E. Gureyev, M. J. Wallace, N. Andres-Thio, K. Uesugi, N. Yagi, and S. B. Hooper, “CT dose reduction factors in the thousands using X-ray phase contrast,” Sci. Rep. 7(1), 15953 (2017).
[Crossref]

Ultramicroscopy (2)

D. Chen, B. Goris, F. Bleichrodt, H. H. Mezerji, S. Bals, K. J. Batenburg, and H. Friedrich, “The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections,” Ultramicroscopy 147, 137–148 (2014).
[Crossref]

W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, “The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography,” Ultramicroscopy 157, 35–47 (2015).
[Crossref]

Other (9)

J. Nocedal and S. J. Wright, Numerical Optimization (Springer Series in Operations Research and Financial Engineering) (Springer, 2000).

P. C. Hansen and J. H. Jørgensen, “Total Variation and Tomographic Imaging from Projections,” 36th Conf. Dutch-Flemish Numer. Anal. Communities Woudschouten (2011).

G. Zang, M. Aly, R. Idoughi, P. Wonka, and W. Heidrich, “Super-Resolution and Sparse View CT Reconstruction,” in Proceedings of the European Conference on Computer Vision (ECCV) (2018), pp. 145–161.

A. C. Kak, M. Slaney, and G. Wang, Principles of Computerized Tomographic Imaging (1988).

A. Chambolle, V. Caselles, M. Novaga, D. Cremers, and T. Pock, “An introduction to Total Variation for Image Analysis,” 9, 263–340 (2009).

V. V. Estrela, H. A. Magalhães, and O. Saotome, “Total Variation Applications in Computer Vision,” arXiv Prepr. arXiv1603.09599 543–570 (2016).

A. Buzmakov, D. Nikolaev, M. Chukalina, and G. Schaefer, “Efficient and effective regularised ART for computed tomography,” in 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (2011), Vol. 2011, pp. 6200–6203.

N. Hasnan, “International Perspectives on Spinal Cord Injury,” (2013).

P. L. Salmon and A. Y. Sasov, “Application of Nano-CT and High-Resolution Micro-CT to Study Bone Quality and Ultrastructure, Scaffold Biomaterials and Vascular Networks,” 323–331 (2007).

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Figures (8)

Fig. 1.
Fig. 1. Micro-XPCT reconstruction of the murine spinal cord (axial view) recorded at 60 keV: (a-b) unstained sample (sample A, lumbar part of spine), pixel size of 3.5 micron, sample-detector distance 2.3 m, (c) sample B (cervical part of spine) perfused with iodine contrast agent, pixel size of 3.5 micron and the sample-detector distance 2.3 m, (d) sample is the same as in Fig. 1(c), pixel size of 1 micron, sample-detector distance 0.6 m. A 50 slices volume of the sample is presented in the figure. ESRF ID17 beamline experiment. The number of tomographic projections was equal to 2000.
Fig. 2.
Fig. 2. (a) Micro-XPCT reconstruction of the vertebrae and spinal cord of the sample A (the cervical part of spine), axial view. Average intensity Z-projection through 50 slices; (b) zoom of the area tagged in Fig. 2(a) with the rectangular frame. Maximum intensity Z-projection through 50 slices. ESRF ID17 beamline experiment. The image was obtained from projections acquired at 30 keV, pixel size of 3.5 micron and the sample-detector distance 2.3 m; the number of tomographic projections was equal to 2000.
Fig. 3.
Fig. 3. (a) Micro-XPCT reconstruction of 50 slices volume (average intensity Z-projection) of the sample A (the cervical part of spine). (b) average intensity Z-projection through a 10 micron thick slab; (c) histological slice with Nissl staining (dark field) of the same area in (b). (a-b) PSI TOMCAT beamline experiment. The projections were acquired at 24 keV, sample-detector distance 0.21 m, pixel size of 1.6 micron; the number of tomographic projections was equal to 1601.
Fig. 4.
Fig. 4. (a) The tomographic image of the spinal cord of the sample A, the same as shown in Fig. 3, (average intensity Z-projection through a 30 micron thick slab). The details, at the white/grey matter interface show features comparable with the micro-vascularization and nerve fibers in the ventral (b) and in the dorsal horns (d). The areas with the ventral and the dorsal horns are shown in (a) with white and red rectangular frames correspondently. Dark field photomicrographs of Nissl-stained 10 micron thick section of the ventral (c) and dorsal horns (e). Red and white arrows are pointed at features comparable with blood vessels and nervous fibers, respectively. (f) Axial view of the spinal cord. Maximum intensity Z-projection through a 30 micron thick slab. The details in a 10 micron thick section show cells in ventral (g) and in the dorsal horns (i) visualized after segmentation. The areas corresponding to the ventral and the dorsal horns are shown in (f) with white and red rectangular frames correspondently. Bright field photomicrographs of Nissl-stained sections of the ventral horn (h) and dorsal horn (j). (a, b, d, f, g, i) PSI TOMCAT beamline experiment. The images were obtained using 24 keV X-rays, sample-detector distance 0.05 m, pixel size of 0.64 micron, the number of tomographic projections was equal to 1601; (c,e,h,j) histological sections.
Fig. 5.
Fig. 5. (a), (b), (c) 3D view of the sample C (the cervical part) perfused with Microfil. The ascending vertebral arteries, partially filled, by the contrast are clearly seen, (c) the unstained small vasculature is virtually segmented and rendered in blue. (d) the sketch of the spine explains the orientation of the samples. (a-c) PSI TOMCAT beamline experiment. The images are obtained at incident energy 24 keV, pixel size of 1.6 micron and the sample-detector distance 0.21 m. The number of tomographic projections is equal to 1601.
Fig. 6.
Fig. 6. (a) Single slice in the axial view of the sample A corresponding to Fig. 2, reconstructed with full data set of 2000 projections; b) the zoom of the area tagged in (a) with the rectangular frame; (c, d) application of RegSIRT with regularization (see Eq. (4)) with sparse data set: (c) 500 angular projections, (d) 100 angular projections; (e) FBP reconstruction with sparse data set of 100 angular projections. RegSIRT allows recovering the morphological information lost by FBP. Pixel size is 3.5 micron.
Fig. 7.
Fig. 7. Convergent rate computed with Eq. (5) in the RegSIRT experiment with (a) 50 and (b) 100 projections.
Fig. 8.
Fig. 8. Convergence rate graphs of regSIRT algorithm on a semilogarithmic scale. Graphs at the left column are calculated with Eq. (5), graphs at the right column is calculated with Eq. (6); (a, b) 50 projections; (c, d) 100 projections; (e, f) 200 projections; (g, h) 500 projections ; (i, j) 1000 projections.

Tables (1)

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Table 1. Experimental parameters used to the imaging of the presented samples.

Equations (6)

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T = μ ( r ) d z = log e ( F 1 1 1 + p 2 u 2 { F { I ( r , z = d ) I 0 } } )
A μ = T
1 2 A μ T 2 min μ
1 2 A μ T 2 + α μ 1 min μ ,
Err k = for pixel in object  ( μ k μ k 1 ) 2 ,
Err k = for pixel in sinogram space  ( A μ k T ) 2

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