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 65 nm for microscopic samples (~75x75 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
X-ray microscopy with 1000 tomograms per second
A team at the Swiss Light Source SLS have set a new record using an imaging method called tomoscopy.
Hierarchical imaging and computational analysis of three-dimensional vascular network architecture in mouse brain
An international team involving researchers from the University and University Hospital Zürich, the Krembil Research Institute and the University and University Hospital in Toronto (Canada), the Department of Physics of Jyväskylä (Finland), the University of Leuven (Belgium), the Johannes Kepler University in Linz (Austria), the Novartis Institutes for Biomedical Research in Emeryville (USA), the ETH Zürich and the Paul Scherrer Institute has developed a protocol that enables hierarchical imaging and computational analysis of vascular networks in entire postnatal- and adult mouse brains, enabling direct and quantitative comparisons of the morphological brain vascular network architecture between different postnatal and / or adult developmental stages. The results have been published on Nature Protocols on September 3rd, 2021.
Understanding Why Solid-State Batteries Fail
Researchers from the University of Oxford, the Diamond Light Source and the Paul Scherrer Institut have generated strong evidence supporting one of two competing theories regarding the mechanism by which lithium metal dendrites grow through ceramic electrolytes. A process leading to short circuit at high rates of charge. The X-ray phase-contrast imaging capabilities of the TOMCAT beamline of the Swiss light source allowed researchers to visualize and characterize the growth of cracks and dendrites deep within an operating solid-state battery. The results were published in Nature Materials on April 22, 2021.
Deep evolutionary origins of the human smile
Detailed characterization of the tooth and jaw structure and development among shark ancestors by synchrotron based X-ray tomographic microscopy at TOMCAT led an international team of researchers from the Naturalis Biodiversity Center in Leiden and the University of Bristol to the discovery that while teeth evolved once, complex dentitions have been gained and lost many times in evolutionary history.
News
TOMCAT welcomes on board two scientists
The X-ray Tomography group welcomes on board Mariana Verezhak and Goran Lovric as members of the TOMCAT beamline crew. They will both contribute to the further development and realization of TOMCAT 2.0 (S- and I-TOMCAT branches on SLS2.0).
SLS 2.0 approved - TOMCAT 2.0 cleared for takeoff!
In December 2020 the Swiss parliament approved the Swiss Dispatch on Promotion of Education, Research and Innovation (ERI) for 2021 to 2024 which includes funding for the planned SLS 2.0 upgrade. The new machine will lead to significantly increased brightness, thus providing a firm basis for keeping the SLS and its beamlines state-of-the-art for the decades to come. The TOMCAT crew is very excited that the TOMCAT 2.0 plans (deployment of the S- and I-TOMCAT branches, see SLS 2.0 CDR, p. 353ff) have been included in the Phase-I beamline upgrade portfolio. These beamlines will receive first light right after the commissioning of the SLS 2.0 machine around mid 2025. A first milestone towards this goal has just been achieved, with the successful installation of the S-TOMCAT optics hutch during W1 of 2021. The TOMCAT scientific and technical staff would like to thank Mr. Nolte and his Innospec crew for delivering perfectly on schedule.
BEATS beamline scientist from SESAME synchrotron trains at TOMCAT
TOMCAT welcomes Gianluca Iori, beamline scientist from BEATS - the new beamline for tomography at the SESAME synchrotron in Jordan, to a 3-month training on beamline operations. Gianluca’s visit is part of the Staff Training (BEATS Work Package 2) organized for BEATS scientific staff and SESAME control engineers. BEATS is a European project, funded under the EU’s Horizon 2020 research and innovation programme and coordinated by the ESRF.
3 new Post Docs and 1 PhD student join TOMCAT
The X-ray Tomography group welcomes Stefan Gstöhl (Post-Doc), Maxim Polikarpov (Post-Doc), Margaux Schmeltz (Post-Doc) and Aleksandra Ivanovic (PhD Student) as new members. The group also thank everybody who helped making it possible for our Post-Docs and PhD student to join PSI amidst the challenges brought by the COVID-19 pandemic.
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.
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