- Full field tomography detection system
- Post-Processing and Reconstructions
Full field tomography detection systemThe standard detection system for full field tomography consists of three main components:
- Optical microscope
- Visible light camera (detector)
Various combinations of different scintillators, microscopes, and cameras are available at TOMCAT to achieve the optimal image quality for a given experimental setup. The choice of equipment depends mainly on the desired magnification, spatial resolution, and field of view, as well as the X-ray energy to be used and the required acquisition speed. The following paragraphs give some technical details and specifications of the available components.
ScintillatorsDepending on user requirements (optimizing for speed and/or resolution), several scintillators are available. The LuAG:Ce scintillators are most frequently used for our standard experiments as they provide a good compromise between speed and resolution. The following table lists the most commonly used scintillators:
Note that the thickness of the scintillator affects the overall spatial resolution! The thicker a scintillator, the poorer the spatial resolution due to light scattering within the scintillator material. The thickness should thus be matched with the effective pixel size of the optical system.
Other scintillator options are available. If you need a specialized setup, please contact beamline staff in advance of your experiments. Users are also welcome to bring their own scintillators, but should contact beamline staff in advance to ensure that the scintillator fits onto the microscope and a proper mount is available and ready to use.
MicroscopesThe TOMCAT endstation features a number of optical microscopes that are compatible with all of our standard detectors. Depending on the detector/microscope combination, the achieved field-of-view can range from 0.4 x 0.3 mm2 to 16.6 x 14.0 mm2. The following table provides a comparison between the microscope characteristics. More detailed information on each microscope is provided below.
Microscope 1: Standard high resolution microscope (Optique Peter)This microscope system is based on diffraction-limited optics and can accommodate 1.25x, 2x, 4x, 10x, 20x and 40x objectives as listed in the table below. The field-of-view and effective pixel sizes are calculated in the standard configuration, i.e., for the pco.EDGE 5.5 detector with a pixel size of 6.5 μm. If a different detector is used, these numbers will change accordingly based on the detector's pixel size.
Please remember that pixel size DOES NOT EQUAL spatial resolution! As a general rule-of-thumb, two pixels are necessary to define an edge and three pixels are necessary to define a feature. So, depending on your goals, the true spatial resolution is typically 2-3 times the effective pixel size.
|Objective||Magnification||Numerical Aperture||Field-of-view (mm2)||Pixel Size (μm2)|
|PLAPO1.25x||1.25||0.06||13.3 x 11.2||5.2 x 5.2|
|PLAPO2x||2||0.08||8.3 x 7.0||3.25 x 3.25|
|UPLAPO4x||4||0.16||4.2 x 3.5||1.63 x 1.63|
|UPLAPO10x||10||0.40||1.7 x 1.4||0.65 x 0.65|
|UPLAPO20x||20||0.70||0.8 x 0.7||0.33 x 0.33|
|UPLAPO40x||40||0.90||0.4 x 0.3||0.16 x 0.16|
Microscope 2: 1:1 Optics (Optique Peter)This system is based on a high numerical aperture tandem 1:1 configuration, accepting a diagonal up to 40 mm. It is typically used for the DPC setup or for large samples that do not require high spatial resolution. A larger pixel size option is available within this setup. Please contact the beamline staff if this option would benefit your experiments.
|Lens||Magnification||Focal length||Field-of-view (mm2)||Pixel Size (μm2)|
|KinoOptik||1.0||150 mm||16.6 x 14.0||6.5 x 6.5|
Microscope 3: 2-4x Continuous Magnification White-Beam Microscope (Elya Solutions)This microscope features a continuously adjustable magnification from 2.24 to 3.78 times, and it is designed with a high numerical aperture and for polychromatic radiation. It is typically used for high-speed experiments with both the pco.EDGE 5.5 and the GigaFRoST detectors, either with monochromatic or polychromatic radiation. The table below lists the approximate range of pixel sizes and fields-of-view attainable within the limits of the magnification for the two different detector types.
|Camera||Magnification||Field-of-view (mm2)||Pixel Size (μm2)|
|pco.EDGE 5.5||2.24||7.4 x 6.3||2.9 x 2.9|
|pco.EDGE 5.5||3.78||4.4 x 3.7||1.7 x 1.7|
|GigaFRoST||2.24||9.9 x 9.9||4.9 x 4.9|
|GigaFRoST||3.78||5.9 x 5.9||2.9 x 2.9|
Microscope 4: High Resolution White-Beam Microscope (Optique Peter)This is a long working distance, high resolution microscope typically used with polychromatic radiation. It is based on diffraction-limited optics and allows the selection of two different magnifications by exchanging the objective lens (5x or 10x). In combination with the 2x eye piece, the effective nominal magnification is 10x or 20x. Removal of the eye piece improves the light throughput significantly, but changes the focal lengths as well. Without the eye piece, the 5x and 10x objective lenses result in effective magnifications of 6.8x and 13.7x, respectively (no longer infinity-corrected).
The two objective lenses are manufactured by Mitutoyo and have the following specs:
The available magnifications and fields-of-view are as follows:
|Objective||Magnification||Numerical Aperture||Focal length [mm]|
|M Plan Apo 10x||5.0||0.14||200|
|M Plan Apo 10x||10.0||0.28||200|
|Camera||Magnification||Field-of-view (mm2)||Pixel Size (μm2)|
|pco.EDGE 5.5||10x||1.7 x 1.4||0.65 x 0.65|
|pco.EDGE 5.5||20x||0.8 x 0.7||0.325 x 0.325|
|pco.EDGE 5.5||6.8x||2.4 x 2.1||0.96 x 0.96|
|pco.EDGE 5.5||13.7x||1.2 x 1.0||0.47 x 0.47|
|GigaFRoST||10x||2.8 x 2.4||1.1 x 1.1|
|GigaFRoST||20x||1.4 x 1.2||0.55 x 0.55|
|GigaFRoST||6.8x||4.1 x 3.5||1.61 x 1.61|
|GigaFRoST||13.7x||2.1 x 1.7||0.80 x 0.80|
DetectorsThe following detectors are routinely in use at TOMCAT and fully supported in the data acquisition and controls system. The choice of detector is governed mostly by the requirements in terms of the achievable pixel size, field of view, image quality and acquisition speed. The table below gives the key specifications for these cameras, while the paragraphs below contain more specific information about each camera model.
|pco.Edge 5.5||pco.Edge 4.2||pco.Dimax||GigaFRoST|
|Pixel size [μm]||6.5||6.5||11.0||11.0|
|Sensor size [pixels] (h x v)||2560 x 2160||2048 x 2048||2016 x 2016||2016 x 2016|
|Sensor size [Megapixels]||5.5||4.2||4.1||4.1|
|Max frame rate (full frame)|| 100 fps (FS,RS)
33 fps (SS,RS)
| 100 fps (FS)
35 fps (SS)
|1255 fps||1255 fps|
|Max frame buffer (full frame)||3'000||3'000||6’307||71’860|
|Exposure time||500μs - 2s||100μs - 10s||2μs - 40ms||2μs - 40ms|
|Dynamic range [dB]||88.6||90.4||65.8||65.8|
|Dark current [e-]||1.2||1.0||<20||<20|
|Cooling||water (chiller)||water (chiller)||air (fan)||air (fan)|
- RS: Rolling Shutter
- GS: Global Shutter
- FS: Fast scan
- SS: Slow scan
pco.Edge 5.5This is the low noise and large field of view camera by pco, and the work-horse camera for standard measurements at TOMCAT. If is built on sCMOS technology and features a sensor size of 2560 x 2160 pixels, 6.5μm pixel size and a 16-bit nominal dynamic range → technical specifications.
pco.Edge 4.2This is the slightly smaller brother of the pco.Edge 5.5, featuring even slightly lower noise levels, but at the expense of a reduced sensor size (2048 x 2048 pixels). It is also based on sCMOS technology with a 6.5μm pixel size and a 16-bit nominal dynamic range → technical specifications.
pco.DimaxThe pco.Dimax is the high-speed camera offered by pco. The imaging chip is built on CMOS technology and features 2016 x 2016 pixels, 11μm pixel size and a 12-bit nominal dynamic range. The camera has an on-board memory of 36 GB and is read out via a USB2.0 connection (slow!) → technical specifications.
This camera is rarely used at present and mostly replaced by the GigaFRoST camera.
GigaFRoSTThe GigaFRoST camere is a PSI in-house development incorporating the same imaging chip as the pco.Dimax, but featuring a novel readout system providing continuous and sustained data streaming at up to ~8GB/s to a dedicated high-performance data backend server. This allows for the high-speed acquisition of long time series to observe dynamic phenomena in a time-resolved manner during long perdiods of time.
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.
Post-Processing and ReconstructionsAll projections are post-processed online and reconstructions are available immediately after a scan is complete. Data can be exported as TIFF (8-bit or 16-bit) or in raw binary format (DMP format) on request. More details about the algorithms and reconstruction capabilities at TOMCAT can be found in:
F. Marone, and M. Stampanoni, "Regridding reconstruction algorithm for real time tomographic imaging", J. Synchrotron Rad., 19, 1029-1037 (2012). pdf