Ptychographic X-ray computed tomography at the nanoscale

Journal name:
Nature
Volume:
467,
Pages:
436–439
Date published:
DOI:
doi:10.1038/nature09419
Received
Accepted

X-ray tomography is an invaluable tool in biomedical imaging. It can deliver the three-dimensional internal structure of entire organisms as well as that of single cells, and even gives access to quantitative information, crucially important both for medical applications and for basic research1, 2, 3, 4. Most frequently such information is based on X-ray attenuation. Phase contrast is sometimes used for improved visibility but remains significantly harder to quantify5, 6. Here we describe an X-ray computed tomography technique that generates quantitative high-contrast three-dimensional electron density maps from phase contrast information without reverting to assumptions of a weak phase object or negligible absorption. This method uses a ptychographic coherent imaging approach to record tomographic data sets, exploiting both the high penetration power of hard X-rays and the high sensitivity of lensless imaging7, 8, 9. As an example, we present images of a bone sample in which structures on the 100nm length scale such as the osteocyte lacunae and the interconnective canalicular network are clearly resolved. The recovered electron density map provides a contrast high enough to estimate nanoscale bone density variations of less than one per cent. We expect this high-resolution tomography technique to provide invaluable information for both the life and materials sciences.

At a glance

Figures

  1. Experimental set-up and sample.
    Figure 1: Experimental set-up and sample.

    a, Schematic of experimental set-up. The X-ray beam (X) impinges on the pinhole (P), which creates a localized illumination on the sample (S). Diffraction patterns are recorded with a two-dimensional pixellated detector D. One out of the 704 diffraction patterns per projection is shown. b, Projection image of the bone specimen as seen on a scintillator screen imaged with a video microscope used for alignment purposes. The scan points indicated by the black dots cover a rectangular area of 40µm×32µm and are placed on concentric circles starting from the centre. c, Scanning electron micrograph of the specimen. Scale bars, 10µm.

  2. Projection images reconstructed from ptychographic data.
    Figure 2: Projection images reconstructed from ptychographic data.

    a, Reconstructed amplitude of the complex object transmission function normalized with respect to air. Artefacts are visible that are attributed to fluctuations in the X-ray intensity. b, Phase part of the complex transmission function. c, Phase after linear-ramp correction and unwrapping. d, Profile along red line in panel a, revealing a low signal-to-noise ratio. e, Profile along red line in panel b, illustrating the wrapping of the phase into the range (−π,π]. f, Profile along red line in panel c. Scale bars, 5µm.

  3. 3D rendering of the tomographic reconstruction.
    Figure 3: 3D rendering of the tomographic reconstruction.

    a,Volume rendering with the bone matrix in translucent colours to show osteocyte lacunae (L) and the connecting canaliculi (C). b, Isosurface rendering of the lacuno-canalicular network obtained by segmenting the corresponding peak in the density on histogram shown in Fig. 4c. Morphological analysis of tomographic reconstructions is most often based on this type of segmentation, which is independent of the absolute scale of the density. Long edges of 3D scale bars, 5µm.

  4. Result of tomographic phase reconstruction.
    Figure 4: Result of tomographic phase reconstruction.

    a, Cut parallel to the rotation axis through the reconstructed volume. The phase values have been converted to quantitative electron density ne (linear greyscale). The labelled structures are air (A), bone matrix (B), canaliculi (C), gallium coating (G), which is a result of focused ion beam preparation, and osteocyte lacuna (L). b, Cut perpendicular to the rotation axis. The two large dark areas are osteocyte lacunae, and small dark dots are sections through individual canaliculi. The slight variations in the shades of grey in a and b indicate inhomogeneity in the bone density at the submicrometre scale. c, Histogram of electron density values in the reconstructed volume (500 equally sized bins for ne values between −0.2 and 1.3Å−3). The labels correspond to the ones in panel a and indicate the grey values that can be associated with the aforementioned features. d, Comparison of the bone peak (label B) of the histogram for two cubic sub-volumes of 1µm3, indicated by the red and blue boxes in a and b. At the micrometre scale, the detection threshold of density fluctuations is slightly less than 0.001Å−3 or about 0.2% of the mean bone density. Scale bars in a and b, 5µm.

References

  1. Yin, G. et al. Energy-tunable transmission x-ray microscope for differential contrast imaging with near 60 nm resolution tomography. Appl. Phys. Lett. 88, 241115 (2006)
  2. Parkinson, D. Y. et al. Quantitative 3-D imaging of eukaryotic cells using soft X-ray tomography. J. Struct. Biol. 162, 380386 (2008)
  3. Haddad, W. S. et al. Ultrahigh-resolution X-ray tomography. Science 266, 12131215 (1994)
  4. Chu, Y. S. et al. Hard-x-ray microscopy with Fresnel zone plates reaches 40 nm Rayleigh resolution. Appl. Phys. Lett. 92, 103119 (2008)
  5. Cloetens, P. et al. Phase objects in synchrotron radiation hard x-ray imaging. J. Phys. D 29, 133146 (1996)
  6. Wilkins, S. W. et al. Phase-contrast imaging using polychromatic hard X-rays. Nature 384, 335338 (1996)
  7. Nugent, K. Coherent methods in the X-ray sciences. Adv. Phys. 59, 199 (2010)
  8. Rodenburg, J. M. Ptychography and related diffractive imaging methods. Adv. Imaging Electron Phys. 150, 87184 (2008)
  9. Thibault, P. et al. High-resolution scanning x-ray diffraction microscopy. Science 321, 379382 (2008)
  10. Davis, T. J. et al. Phase-contrast imaging of weakly absorbing materials using hard X-rays. Nature 373, 595598 (1995)
  11. Nugent, K. et al. Quantitative phase imaging using hard X rays. Phys. Rev. Lett. 77, 29612964 (1996)
  12. Momose, A. et al. Phase-contrast X-ray computed tomography for observing biological soft tissues. Nature Med. 2, 473475 (1996)
  13. Pfeiffer, F. et al. Phase retrieval and differential phase-contrast imaging with low-brilliance X-ray sources. Nature Phys. 2, 258261 (2006)
  14. Faulkner, H. M. & Rodenburg, J. M. Movable aperture lensless transmission microscopy: a novel phase retrieval algorithm. Phys. Rev. Lett. 93, 023903 (2004)
  15. Rodenburg, J. et al. Hard-x-ray lensless imaging of extended objects. Phys. Rev. Lett. 98, 034801 (2007)
  16. Guizar-Sicairos, M. & Fienup, J. R. Phase retrieval with transverse translation diversity: a nonlinear optimization approach. Opt. Express 16, 72647278 (2008)
  17. Giewekemeyer, K. et al. Quantitative biological imaging by ptychographic x-ray diffraction microscopy. Proc. Natl Acad. Sci. USA 107, 529534 (2010)
  18. Dierolf, M. et al. Ptychographic coherent diffractive imaging of weakly scattering specimens. N. J. Phys. 12, 035017 (2010)
  19. Schropp, A. et al. Hard x-ray nanobeam characterization by coherent diffraction microscopy. Appl. Phys. Lett. 96, 091102 (2010)
  20. Vine, D. J. et al. Ptychographic Fresnel coherent diffractive imaging. Phys. Rev. A 80, 063823 (2009)
  21. Morrison, G. R. & Chapman, J. N. A comparison of three differential phase contrast systems suitable for use in STEM. Optik 64, 112 (1983)
  22. Schneider, P. et al. Towards quantitative 3D imaging of the osteocyte lacuno-canalicular network. Bone doi:10.1016/j.bone.2010.07.026 (2010)
  23. Kamioka, H. et al. A method for observing silver-stained osteocytes in situ in 3-m sections using ultra-high voltage electron microscopy tomography. Microsc. Microanal. 15, 377383 (2009)
  24. Hubbell, J. & Seltzer, M. Tables of X-ray Mass Attenuation Coefficients and Mass Energy-Absorption Coefficients. Version 1.4, Report NISTIR-5632 (National Institute of Standards and Technology, 1995) left fencehttp://physics.nist.gov/xaamdiright fence.
  25. Chapman, H. N. et al. High-resolution ab initio three-dimensional x-ray diffraction microscopy. J. Opt. Soc. Am. A 23, 11791200 (2006)
  26. Nishino, Y. et al. Three-dimensional visualization of a human chromosome using coherent x-ray diffraction. Phys. Rev. Lett. 102, 018101 (2009)
  27. Howells, M. et al. An assessment of the resolution limitation due to radiation-damage in X-ray diffraction microscopy. J. Electron Spectrosc. Relat. Phenom. 170, 412 (2009)
  28. Kraft, P. et al. Performance of single-photon-counting PILATUS detector modules. J. Synchrotron Radiat. 16, 368375 (2009)
  29. Thibault, P. et al. Probe retrieval in ptychographic coherent diffractive imaging. Ultramicroscopy 109, 338343 (2009)
  30. Ghiglia, D. C. & Pritt, M. D. Two-Dimensional Phase Unwrapping: Theory, Algorithms And Software (Wiley, 1998)

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Author information

Affiliations

  1. Department of Physics (E17), Technische Universität München, 85748 Garching, Germany

    • Martin Dierolf,
    • Pierre Thibault &
    • Franz Pfeiffer
  2. Swiss Light Source, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland

    • Andreas Menzel,
    • Cameron M. Kewish &
    • Oliver Bunk
  3. Institute for Biomechanics, ETH Zurich, 8093 Zurich, Switzerland

    • Philipp Schneider
  4. Electron Microscopy ETH Zurich (EMEZ), 8093 Zurich, Switzerland

    • Roger Wepf
  5. Present address: Synchrotron SOLEIL, Saint-Aubin BP-48, 91192 Gif-sur-Yvette, France.

    • Cameron M. Kewish

Contributions

A.M., R.W., M.D., P.T., O.B., and F.P. conceived the experiment. R.W. prepared the sample. A.M., C.M.K., P.T., M.D., O.B. and F.P. carried out the experiment. P.T., M.D., C.M.K. and P.S. analysed the data. All authors discussed the results and contributed to the final manuscript.

Competing financial interests

The authors declare no competing financial interests.

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Supplementary information

PDF files

  1. Supplementary Information (274K)

    The file contains Supplementary Figure 1 and legend, legends for Supplementary Movies 1-6 and an additional reference.

Movies

  1. Supplementary Movie 1 (9.2M)

    This movie shows reconstructed projections: amplitude (left), raw phase (centre), unwrapped phase (right) - see Supplementary Information file for full legend.

  2. Supplementary Movie 2 (9.5M)

    This movie shows sinograms calculated from amplitude and unwrapped phase projections - see Supplementary Information file for full legend.

  3. Supplementary Movie 3 (9M)

    This movie shows volume rendering of the reconstructed bone density - see Supplementary Information file for full legend.

  4. Supplementary Movie 4 (9.5M)

    This movie shows slices of tomographic volume perpendicular to the rotation axis - see Supplementary Information file for full legend.

  5. Supplementary Movie 5 (10.8M)

    This movie shows slices of tomographic volume in one of the directions parallel to the rotation axis - see Supplementary Information file for full legend.

  6. Supplementary Movie 6 (10.8M)

    This movie shows slices of tomographic volume parallel to the rotation axis and perpendicular to the slices in Movie 5 - see Supplementary Information file for full legend.

Additional data