PMC:7473770 / 34621-39069
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7473770","sourcedb":"PMC","sourceid":"7473770","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7473770","text":"Phase contrast tomography\nFor Covid-19 lung tissue, the scans were recorded at the GINIX endstation of the PETRA III storage ring (DESY, Hamburg). The projections were acquired at two different photon energies Eph, 8keV and 13.8keV, using the first and third harmonic of the 5 m P10 undulator and a Si(111) channel-cut monochromator, respectively. Data are shown here only for 8keV, which gave highest contrast for the unstained lung tissue. Two tomography configurations were combined to cover a larger range of length scales:\n\n(1–parallel beam)\nRecordings with the unfocused quasi-parallel beam illumination and a high resolution microscope detection system, resulting in in a FOV of 1.6 mm sampled at a pixel size of 650 nm.\n\n(2–cone beam)\nHolographic recordings with the divergent and coherence filtered beam emanating from a compound focusing system composed of a Kirkpatrick-Baez (KB) mirrors system and an x-ray waveguide, resulting in a FOV of 0.4 mm sampled at a pixel size of about 167 nm (depending on exact geometry).\nBoth configurations were implemented side-by-side, using the same fully-motorized tomography stage and mounting, as detailed in Frohn et al., 2020. A sketch of both configurations is shown in Figure 1 . First, parallel-beam overview scans were acquired of the entire tissue volume embedded in paraffin. To this end a 3.5 mm biopsy punch was taken from the multi-sample tissue block, and then scanned in a stitching-mode yielding a large overview reconstruction, composed of up to 20 individual tomograms (depending on tissue size). To increase image quality and avoid artifacts related to region-of-interest (ROI) or local tomography, a selected 1 mm punch was then taken from the already scanned larger tissue cylinder, and re-scanned, first in the parallel- and then the cone-beam geometry. Experimental and acquisition parameters used for the data shown are listed in Table 3.\nTable 3. Data acquisition parameters for x-ray phase-contrast tomography measurements.\nCone geometry Parallel geometry\nFOV 0.4 mm × 0.35 mm 1.6 mm × 1.4 mm\nPixel size 167 nm 650 nm\nz 01 125 mm -\nz 12 4975 mm 10 mm − 100 mm\nRegime holographic direct contrast\nRotation start-stop continuous\nExposure 2 s 0.035 s\nTotal exposure ≃ 63 m i n ≃ 75 s\nVolumetric flowrate 1.16 × 10 4 μ m / 3 s 3.75 × 10 7 μ m / 3 s The configuration for (1–parallel beam) is depicted in Figure 1c. The high-resolution microscope detection system (Optique Peter, France) was based on a 50μm thick LuAG:Ce scintillator imaged with a 10× magnifying microscope objective onto a sCMOS sensor (pco.edge 5.5, PCO, Germany), resulting in an effective pixel size of 0.65μm. The high photon flux density allowed for image acquisition with continuous motor movement, short acquisition time of 35 ms per frame, and a framerate of 20 fps. Single-distance tomogram recordings with about 1500 projections, and flat images before and after the scan, took less than 2 min. For these scans, the focusing optics (KB-mirrors and waveguide) as well as the fastshutter (Cedrat technologies) were moved out of the beam, and beam size was adjusted by the upstream slit systems. To avoid detector saturation, the beam was attenuated by 4× single crystal silicon wafers.\nThe configuration for (2–cone beam) is depicted in Figure 1d: The beam was focused by the KB-mirrors to about 300 nm. To further reduce the secondary source size, to increase coherence, and to achieve a smooth wavefront for holographic illumination, an x-ray waveguide formed by 1 mm long lithographic channels in silicon with a cross-section of about 100 nm was positioned in the focal plane of the KB-mirrors, resulting in an exit flux of 1–4⋅109 photon/s (depending on alignment and storage ring), as measured with the single photon counting detector (Pilatus, Dectris). The sample was positioned at variable (defocus) distances behind the focus (waveguide exit), typically z01=125mm for the first distance. The geometrically magnified holograms were recorded by a fibre-coupled sCMOS sensor (Zyla HF 5.5 detector, Andor Technologies) with a customized 15μm thick Gadox scintillator, and 6.5μm pixel size. The detector position at about z02=5100mm behind the focus resulted in a magnification of about M=41 (for the first defocus distance), and hence an effective pixel size of 167 nm. 1442 projections were recorded, with a typical exposure time of 2 s per 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