TOMCAT - X02DA: Tomographic Microscopy
A beamline for TOmographic Microscopy and Coherent rAdiology experimenTs
The beamline for TOmographic Microscopy and Coherent rAdiology experimentTs (TOMCAT) [1] is operated by the X-ray Tomography Group and 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.
| 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 |
Scientific Highlights
3D printing silica aerogels at the micrometer scale
A group of EMPA and ETH Zürich researchers have developed a new method to directly write ink made of silica aerogels in 3D. Thanks to X-ray phase contrast tomography at the TOMCAT beamline they characterized the resulting printed material with different compositions. Their results were published in Nature on August 18, 2020.
Phase contrast microtomography reveals nanoparticle accumulation in zebrafish
Metal-based nanoparticles are a promising tool in medicine – as a contrast agent, transporter of active substances, or to thermally kill tumor cells. Up to now, it has been hardly possible to study their distribution inside an organism. Researchers at the University of Basel in collaboration with the TOMCAT team have used phase contrast X-ray tomographic microscopy to take high-resolution captures of the nanoparticle aggregation inside zebrafish embryos.
The study was published in the journal Small and featured on the cover of its current issue.
Miniaturized fluidic circuitry observed in 3D
The team of Prof. Thomas Hermans at the University of Strasbourg in France managed to create wall-less aqueous liquid channels called anti-tubes. Thanks to X-ray phase contrast tomography at the TOMCAT beamline those anti-tubes could be observed in 3D. The exciting results were published in Nature on May 6, 2020.
X-ray Imaging for Biomedicine: Imaging Large Volumes of Fresh Tissue at High Resolution
The TOMCAT beamline at the Swiss Light Source specializes in rapid high-resolution 3-dimensional tomographic microscopy measurements with a strong focus on biomedical imaging. The team has recently developed a technique to acquire micrometer-scale resolution datasets on the entire lung structure of a juvenile rat in its fresh natural state within the animal’s body and without the need for any fixation, staining or other alteration that would affect the observed structure (E. Borisova et al., 2020, Histochem Cell Biol).
News
Automatic extraction of dynamic features from sub-second tomographic microscopy data
A fully automatized iterative reconstruction pipeline designed to reconstruct and segment dynamic processes within a static matrix has been developed at TOMCAT. The algorithm performance is demonstrated on dynamic fuel cell data where it enabled automatic extraction of liquid water dynamics from sub-second tomographic microscopy data. The work is published in Scientific Reports on 2 October 2020.
4 times compression factor for tomographic data feasible
In a recent study, TOMCAT has shown that lossy compression by a factor of at least 3 to 4 of raw acquisitions generally does not affect the reconstruction quality and that higher factors (six to eight times) can be achieved for tomographic volumes with a high signal-to-noise ratio as it is the case for phase-retrieved datasets. This finding is relevant to current challenges on large tomography data management and storage especially at synchrotron facilities. The results of this study was published in Journal of Synchrotron Radiation.
Rapid 3D directional small-angle scattering imaging achieved at TOMCAT
Researchers from the TOMCAT beamline have developed a small-angle scattering tensor tomography method to visualize microscopic features within a macroscopic field of view with unprecedented data acquisition speed. The results of the study were published in Applied Physics Letters on April 1, 2020.
Towards dynamic feedback control during time-resolved CT at TOMCAT
Researchers from the CWI in Amsterdam and the TOMCAT beamline have developed and implemented a real-time CT reconstruction, visualisation, and on-the-fly analysis approach to monitor dynamic processes as they occur. With processes of multiple sets of CT slices per second, this represents the next crucial step towards adaptive feedback control of time-resolved in situ tomographic experiments. The results of this study were published in Scientific Reports on December 5, 2019.
High-numerical-aperture optics is key to ultra-fast tomographic microscopy
A novel high-numerical-aperture macroscope optics dedicated to high-temporal and high-spatial resolution X-ray tomographic microscopy is available at TOMCAT. Coupled with the in-house developed GigaFRoST camera, this highly efficient imaging setup enables tomographic microscopy studies at 20 Hz and beyond, opening up new possibilities in tomographic investigations of dynamic processes. A detailed characterization of the macroscope performance was published in Journal of Synchrotron Radiation on May 21, 2019.
From whole organ imaging down to single cell analysis
Researchers from the TOMCAT beamline, University College London (UCL), IDIBAPS and Universitat Pompeu Fabra (UPF) have developed a methodology that allows the multiscale analysis of the structural changes resulting from remodelling cardiovascular diseases, from whole organ down to single-cell level. This methodology has been published as an article in the journal Scientific Reports on May 6th 2019.
PSI Thesis Medal goes to Dr. Matias Kagias
The PSI Thesis Medal is awarded every second year to the best PhD thesis performed at the Paul Scherrer Institut. Matias received the prize for his excellent thesis entitled "Direct Self-Imaging Methods for X-ray Differential Phase and Scattering Imaging". Congratulations!
TOMCAT paper on hard X-ray multi-projection imaging published
The TOMCAT team in collaboration with scientists from CFEL, MaxIV and ESRF developed a method for hard X-ray multi-projection imaging, using a single crystal to split the beam into multiple beams with different directions.
References
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- F. Marone, and M. Stampanoni, "Regridding reconstruction algorithm for real time tomographic imaging", J. Synchrotron Rad., 19, 1029-1037 (2012). DOI: 10.1107/S0909049512032864
- 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