TOMCAT - X02DA: Tomographic Microscopy

A beamline for TOmographic Microscopy and Coherent rAdiology experimenTs

The beamline for TOmographic Microscopy and Coherent rAdiology experimentTs (TOMCAT) [1] offers cutting-edge technology and scientific expertise for exploiting the distinctive peculiarities of synchrotron radiation for fast, non-destructive, high resolution, quantitative investigations on a large variety of samples. Absorption-based and phase contrast imaging are routinely performed with isotropic voxel sizes ranging from 0.16 to 11 μm (fields-of-view (h x v) of 0.4 x 0.3 mm2 and 22 x 3-7 mm2, respectively) in an energy range of 8-45 keV. Phase contrast is obtained with simple edge-enhancement, propagation-based techniques [2, 3] or through grating interferometry [4]. 

Typical acquisition times are on the order of seconds to a few minutes. However, dynamic processes can be followed in 4D (3D space + time) using the ultra-fast endstation, which provides sub-second temporal resolution [5] for extended time periods thanks to the in-house developed GigaFRoST system [6]. A laser-based heating system [7] and a cryojet and cryo-chamber are available as standard installations and are compatible with both the standard and ultra-fast endstations. It is also possible to bring specialized, user-defined instrumentation to TOMCAT. Please contact beamline staff in advance to discuss this option. 

A temporal resolution of a few (< 5) minutes can also be achieved with the hard X-ray full-field microscope setup [8] delivering a pixel size of 80 nm for microscopic samples (~50x50 μm2 field-of-view).

3D tomographic datasets are reconstructed from 2D projections using highly optimized software [9, 10] based on Fourier methods and a user-friendly interface (i.e., an ImageJ plug-in). Remote access to a flexible HPC facility is available for subsequent advanced post-processing and data quantification. A suite of analytical and iterative reconstruction routines is provided, additional ad-hoc tools can be easily installed by the single user.


14 September 2018

New TOMCAT paper

Our team in collaboration with scientists from CFEL, MaxIV and ESRF published a work presenting a method for hard X-ray multi-projection imaging. The idea is to split the main beam from a synchrotron or, in the future, from a X-FEL, into multiple beams in order to acquire simultaneous, angularly spaced projection of a sample. This approach provides multiple angular views of the specimens and can provide volumetric information of natural processes and non-reproducible samples in a single shot.

1 December 2017

Arttu Miettinen joins the TOMCAT team as PostDoc

After his PhD at the University of Jyväskylä in Finnland in image analysis, Arttu will be working on the stitching and segmentation of large datasets in the framework of the Human Brain Project.
News Archive

Technical Data

Energy range 8-45 keV
Highest 3D spatial resolution ca. 1 μm in parallel beam geometry
ca. 200 nm in full-field geometry
Max. temporal resolution 20 Hz
Available techniques - Absorption-based tomographic microscopy
- Propagation-based phase contrast tomographic microscopy
- Ultra-fast tomographic microscopy
- Grating interferometry
- Absorption and phase contrast nanotomography
Available devices for in situ sample conditioning - Laser-based heating system
- Cryojet and cryo-chamber

  1. M. Stampanoni, A. Groso, A. Isenegger, G. Mikuljan, Q. Chen, A. Bertrand, S. Henein, R. Betemps, U. Frommherz, P. Bohler, D. Meister, M. Lange, and R. Abela, "Trends in synchrotron-based tomographic imaging: the SLS experience", Developments in X-Ray Tomography V, Proceedings of the Society of Photo-Optical Instrumentation Engineers (Spie), 6318, U199-U212 (2006). DOI: 10.1117/12.679497
  2. A. Groso, R. Abela, and M. Stampanoni, "Implementation of a fast method for high resolution phase contrast tomography", Optics Express, 14, 8103-8110 (2006). DOI: 10.1364/OE.14.008103
  3. 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). DOI: 10.1046/j.1365-2818.2002.01010.x
  4. S. A. McDonald, F. Marone, C. Hintermüller, G. Mikuljan, C. David, F. Pfeiffer, and M. Stampanoni, "Advanced phase-contrast imaging using a grating interferometer", J. Synchrotron Rad., 16, 562-572 (2009). DOI: 10.1107/S0909049509017920
  5. R. Mokso, F. Marone, D. Haberthur, J. C. Schittny, G. Mikuljan, A. Isenegger, and M. Stampanoni, "Following Dynamic Processes by X-ray Tomographic Microscopy with Sub-second Temporal Resolution", 10th International Conference on X-Ray Microscopy, 1365, 38-41 (2011). DOI: 10.1063/1.3625299
  6. 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
  7. J. L. Fife, M. Rappaz, M. Pistone, T. Celcer, G. Mikuljan, and M. Stampanoni, "Development of a laser-based heating system for in-situ synchrotron-based x-ray tomographic microscopy", J. Synchrotron Rad., 19, 352 (2012). DOI: 10.1107/S0909049512003287
  8. M. Stampanoni, R. Mokso, F. Marone, J. Vila-Comamala, S. Gorelick, P. Trtik, et al., "Phase-contrast tomography at the nanoscale using hard x-rays", Physical Review B, 81, 140105R (2010). DOI: 10.1103/PhysRevB.81.140105
  9. F. Marone, and M. Stampanoni, "Regridding reconstruction algorithm for real time tomographic imaging", J. Synchrotron Rad., 19, 1029-1037 (2012). DOI: 10.1107/S0909049512032864
  10. F. Marone, A. Studer, H. Billich, L. Sala, and M. Stampanoni, "Towards on-the-fly data post-processing for real-time tomographic imaging at TOMCAT", Advanced Structural and Chemical Imaging, 3, 1 (2017). DOI: 10.1186/s40679-016-0035-9