Imaging Techniques at TOMCAT

X-ray Tomographic Microscopy

X-ray tomographic microscopy is a powerful technique used to visualize and study the three dimensional (3D) internal structure and material properties of a variety of optically opaque samples in a nondestructive manner. Computed tomography (CT) was introduced in 1973 by Houndsfield [1] and initially applied mostly in the medical field, where it is now well established. With time it became clear that CT is an excellent tool for the investigation of a wider range of specimens and with the advancement of X-ray source and detector technology the achievable spatial resolution reached the micro- (and nano-) meter range. Nowadays, most academic and industrial research departments in many fields such as materials, food, pharmaceuticals, environmental and Earth sciences, are equipped with laboratory based microCT systems, which are routinely used for the nondestructive analysis of the internal microstructure of the most diverse samples.  

In X-ray tomographic microscopy, radiographic projections of a sample are acquired. The most widely exploited contrast mechanism is the selective attenuation of the X-ray beam traveling through the sample. For a given beam energy, the number of absorbed photons depends on the sample material (Z-number and electron density): the larger these parameters, the more photons absorbed. Other contrast mechanisms (e.g. phase contrast), rooting to different X-ray matter interaction processes, can also be utilized. 

Radiographic projections, however, only provide 2D cumulative information of the structure along the beam path. From a single radiographic projection (Fig. 1, left), it is not possible to determine whether the beam was mostly attenuated when entering or exiting the sample, or maybe homogeneously along its trajectory through the sample. 3D internal structural details (Fig. 1, right) can be revealed by taking radiographs at different sample orientations and combining those using sophisticated mathematical algorithms for tomographic reconstructions based on Fourier analysis (e.g., filtered back-projection) or iterative methods.  
 

projection vs slice
Figure 1. (Left) An X-ray radiograph showing a 2D projection the sample’s X-ray absorption. (Right) A reconstructed tomographic slice across the red dashed line indicated on the left. A collection of tomographic slices along the full height of the radiograph on the left constitutes a 3D map of the sample’s X-ray absorption. (Source: )

Knowledge provided by X-ray tomographic microscopy on the interior of optically opaque objects is immense. In addition to the mere visualization of the 3D internal structural details, extraction of quantitative information is now possible thanks to the ever increasing computational power. Number, size, shape, orientation, spatial distribution, connectivity and packing of features of interest in the analyzed volume are just a few of the possible quantitative metrics which can be extracted from tomographic datasets. If adequate calibration measurements are performed, X-ray tomographic microscopy can also provide insight into composition (e.g., bone mineralization). 

Advantages of Synchrotron Radiation

At third generation synchrotron sources, thanks to a very intense and coherent beam, X-ray imaging has experienced a true revolution. The tremendous photon density reached by these sources brings huge advantages with respect to traditional X-ray laboratory instruments. The high brilliance of synchrotron light provides increased spatial and temporal resolution: detection of details as small as 1 micron in millimeter-sized samples is routinely possible within only a few minutes. In addition, the monochromaticity of the X-ray beam makes quantitative measurements of material properties possible and vastly simplifies the identification of different phases, since beam hardening artifacts, distinctive for laboratory setups, can be avoided. Increased contrast and reduced noise are also promoted by the monochromatic beam and the high photon flux. Furthermore, the spatial coherence peculiar to synchrotron radiation enables, using different phase contrast techniques, to boost contrast in low absorbing or similar Z-number materials, such as soft tissue. Phase contrast leverages on the refraction of the beam interacting with the sample and the resulting interference phenomena. Moreover the almost parallel beam geometry usual at tomographic microscopy endstations at synchrotron sources permits the accurate reconstruction of tomographic volumes without cone beam artifacts. The combination of these factors contributes to the astonishing quality of the resulting images. 

Finally the latest detector generation based on CMOS technology coupled with the highly brilliant synchrotron radiation has made sub-second temporal resolution a reality. In this way, previously unimaginable new science and experiments, where fast dynamic processes can be captured for the first time in 3D through time [2], are now possible. 

The new fourth generation X-ray sources, such as the SLS 2.0 machine, will provide an even brighter and more coherent beam boosting image quality to an unprecedented level and unlocking for the first time simultaneous higher spatial and temporal resolutions, pushing dynamic tomographic imaging towards unexplored frontiers.

References

  1. G. N. Hounsfield, Computerized transverse axial scanning (tomography): Part 1. Description of system, Br J Radiol, 46, 1016-1022 (1973).
  2. R. Mokso, D. A. Schwyn, S. M. Walker, M. Doube, M. Wicklein, T. Müller, M. Stampanoni, G. K. Taylor, and H. G. Krapp, "Four-dimensional in vivo X-ray microscopy with projection-guided gating", Scientific Reports 5, 8727 (2015).

 

The selective attenuation of the X-ray beam traversing a sample, at energies below 100 keV mainly a manifestation of the photoelectric effect discovered by Albert Einstein, is the most exploited and widespread contrast mechanism for X-ray imaging. The probability (or cross-section spe) of such a photoelectric interaction to happen is strongly dependent on the Z number of the material (Z4) and on the energy of the X-ray photons (E-3) used. Thanks to these strong dependencies, high contrast between different materials can be achieved, if the beam energy is tuned for an optimized X-ray beam transmission of about 30%. In general, highest contrast is achieved at low photon energies for high-atomic-number materials, while contrast is limited at high photon energies and for lighter materials or materials with similar Z numbers.
 
The X-ray beam is not only attenuated while traversing a sample. It is also refracted at interfaces between different material domains as a consequence of the retardation of the phase of the wave travelling through the object. The complex index of refraction for X-rays is only slightly deviating from unity, therefore the resulting refraction angles are very small. If these minute trajectory deviations can be sensed, they can provide complementary information to attenuation and significantly boost the image contrast at high energies and for materials with similar Z numbers. 
 
In contrast to most conventional X-ray sources, X-ray radiation at third and fourth generation facilities has a significant degree of coherence, meaning that interference phenomena can occur and can potentially be observed. The refracted and unrefracted X-ray beams traversing the sample do indeed interfere downstream of the specimen. This interference manifests itself as intensity Fresnel fringes at the interfaces between different homogeneous domains on a projection image of the irradiated sample. The observed so-called edge enhancement increases when increasing the distance between the sample and the detector (Figure 1 – Top row), significantly augmenting the sample visibility. Simple edge enhancement has proved valuable for the non-destructive study of the internal structures of different samples, but despite the increased edge visibility, the contrast between domains in the acquired projections as well as in the tomographic reconstructions remains unchanged and low for materials with similar Z numbers (Figure 1 - Top and middle row). The contrast in soft and low-absorbing materials can be boosted by using phase retrieval algorithms (e.g. [1]) on the acquired radiographic projections prior to tomographic reconstruction (Figure 1 - Bottom row). Propagation-based phase-contrast X-ray imaging, with and without phase retrieval, is available at TOMCAT. More advanced phase contrast techniques relying on the refraction of the X-ray beam also exist, but either require additional hardware (e.g. gratings [2], crystals [3]) or multiple datasets per sample [4] and are usually not offered at TOMCAT.
propagation-based phase contrast
Figure 2. X-ray imaging of a zebra fish at the TOMCAT beamline (21 keV, 0.65 µm pixel size) for different sample-detector distances D. (Top) Flat- and dark-field corrected radiographic projections, (middle) coronal slices through the absorption contrast tomographic volume, and (bottom) coronal slices through the tomographic volume reconstructed after single distance phase-retrieval [1].

References

  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”, Journal of Microscopy 206, 33-40 (2002)
  2. T. Weitkamp, A. Diaz, C. David, F. Pfeiffer, M. Stampanoni, P. Cloetens, and E. Ziegler, “X-ray phase imaging with a grating interferometer”, Optics Express 13(16), 6296-6304 (2005)
  3. D. Chapman, W. Thomlinson, R. E. Johnston, D. Washburn, E. Pisano, N. Gmur, et al., “Diffraction enhanced x-ray imaging”, Physics in Medicine and Biology 42(11), 2015-2025 (1997)
  4. P. Cloetens, W. Ludwig, J. Baruchel, D. Van Dyck, J. Van Landuyt, J. P. Guigay, and M. Schlenker, “Holotomography: Quantitative phase tomography with micrometer resolution using hard synchrotron radiation x rays”, Applied Physics Letters 75(19), 2912-2914 (1999)

TOMCAT offers world-leading capabilities for a continuous, ultra-fast acquisition of tomographic datasets. The dynamic evolution of samples under in situ, operando, or in vivo conditions can be investigated by measuring a rapid series of 3D volume data sets as a function of time (4D dataset). Individual 3D volume data sets consisting of hundreds to thousands of radiographic projections can be measured in typically well under one second, and thanks to the in-house development of the GigaFRoST high-speed camera and readout system, the total duration of data acquisition is no longer limited by the on-board camera memory. Data are streamed directly to a data acquisition server providing a high data throughput of nearly 8 GB/s, real-time preview capabilities, as well as sophisticated protocols for triggering, gating, and selective storage of data.

The high-speed setup is compatible with the usual absorption and single distance propagation-based phase contrast tomography modalities. In practice, phase contrast is almost always the contrast mechanism of choice since it yields much better contrast for the typically very noisy and low intensity data acquired at high frame rates. Data can be acquired either using the high bandwidth monochromatic beam from the multilayer monochromator, or using a filtered white beam providing even more flux and, in particular, a significant flux increase at higher energies. The GigaFRoST camera is, in principle, compatible with all of the TOMCAT microscope choices (see the section on Detectors), though in practice the white beam microscopes are used much more often than those for monochromatic beam. Naturally, the necessary acquisition time increases when choosing smaller pixel sizes.

Typical detector frame rates for the fast measurements range from 1 kHz at full frame to up to 20 kHz using a reduced region of interest (ROI) on the detector. The achievable frame rates and the associated maximum number of frames that fit into the server memory (512 GB) and the total acquisition time compared to the commercially available pco.Dimax camera are listed in the following table:

ROI size(hxv)

Max. frame rate

#frames
pco.Dimax
(36 GB RAM)

#frames
GigaFRoST
(512 GB RAM)

Total recording time

 

5 sec

57.3 sec

2016 x 2016

1’255

6’307

71’860

2016 x 1008

2’490

~12’614

143’720

1920 x 1080

2’424

12’362

140’844

1008 x 1008

4’305

25’037

287’440

672 x 540

10’288

~ 70’100

804’832

480 x 288

21’907

~185’430

2’112’684

240 x 240

33’875

~445’036

2’621’440

For an in-depth description of the GigaFRoST camera system refer to R. Mokso, C. M. Schlepütz, G. Theidel, H. Billich, E. Schmid, T. Celcer, et al., "GigaFRoST: The Gigabit Fast Readout System for Tomography", J. Synchrotron Rad., 24 (6), 1250-1259 (2017). DOI: 10.1107/S1600577517013522.

Endstation 1 can accommodate various user-built sample environments (for example, compression or tensile rigs, heating or cooling stages, electrochemical sample cells, etc.) as well as the TOMCAT laser furnace for high temperature studies. Please contact beamline staff to discuss your experimental ideas and requirements in detail.

More technical information about the end station capabilities for time-resolved tomography can be found in the following article: G. Lovrić, R. Mokso, C. M. Schlepütz, and M. Stampanoni, "A multi-purpose imaging endstation for high-resolution micrometer-scaled sub-second tomography", Physica Medica, 32, 1771 (2016). DOI: 10.1016/j.ejmp.2016.08.012

Linking micrometer and nanometer scales, the TOMCAT nanoscope was commissioned in 2009. Based on Zernike phase contrast, this full-field microscope is composed of:

  • a condenser: a custom designed beamshaper producing a top-flat illumination in the focal plane
  • a series of Fresnel Zone Plates (FZP) objectives, with different diameters on the same frame (to be selected according to the working energy)
  • phase dots (optional) placed at the back-focal distance of the FZP to generate Zernike phase contrast.

The detector, placed downstream about 10 m, records the magnified phase contrast image of the sample. The field-of-view is from about 75um2.

Thanks to the latest improvements in optical design, specifically with regards to the beamshaper and the Fresnel Zone Plate, as well as on the hardware of the setup itself to produce higher stability, we are now able to use the nanoscope from 8 keV to 20 keV in multilayer or Silicon Monochromatique mode, leading to a pixel size down to 65nm (approximately 150/200 nm spatial resolution). The setup can be used in absorption or phase contrast mode for a wide range of applications, including biology, geology, materials science, and paleontology.
 

The TOMCAT nanoscope: a hard X-ray full field energy tunable TXM
The TOMCAT nanoscope: a hard X-ray full field energy tunable TXM

For further information, please see:

  1. Stampanoni M. et al. (2009). J. Phys.: Conf. Ser. 186, 012018. DOI
  2. Zernike F. (1934). Physica 1, 689. DOI
  3. Stampanoni M. et al. (2010). Physical Review B 81, 140105. DOI
  4. Jefimovs K. et al. (2008). J. Synchrotron Radiation 15, 106. DOI
  5. Vartiainen I. et al. (2014). Opt. Lett. 39, 1601. DOI