Appendix 3
Further datasets
Controls: The imaging workflow was also applied to hydrated and/or healthy lung tissue as a control. First, overview scans covering the entire samples were recorded. Then, hydrated 1 mm biopsy punches (two for CTRLI, one for CTRLII and CTRLIII, where CTRLII and CTRLIII are from the same patient) were recorded in (1 - parallel beam) configuration. Biopsy punches from CTRLII and CTRLIII were also examined in (2 - cone beam) mode. Appendix 3—figure 1 presents (a) the rendering of the hydrated control, and (b,c) virtual slices through the reconstruction volume, showing the lung parenchymal architecture in healthy control tissue. UA-stained samples: For all Covid-19 patients, autopsies were also treated by UA-staining in order to increase the contrast. Stitched overview scans in (1 - parallel beam) configuration were recorded, similar to Figure 3. From the UA-labeled tissue blocks of patients I, III, IV and V, 1 mm, biopsy punches were than scanned in the same configuration (Figure 4). Using the (2 - cone beam) setup, these samples from I, III and IV were imaged at 8.0⁢keV x-rays, while V was examined at 13.8⁢keV, as shown for Figure 5. Variation of propagation distance: Scans of the unstained tissue block from patient II were recorded at different propagation distances (z12=50, 100 and 125keV) and different x-ray energies (13.3, 13.8, 14.3 and 14.8 keV). In cone-beam configuration, the unstained biopsy punch from patient I was scanned at 13.8⁢keV x-rays. Compact μCT scans: Prior to the synchrotron experiment, some of the samples have been examined with a laboratory phase-contrast μCT-setup in large mm2-sized FOV-configuration (Liquid metal jet source, Kα=9.5keV, pxeff=5μm, z12=1.7m, 1200 projections of 1 s exposure time with a flat panel CMOS detector with 150⁢μ⁢m Gadox-scintillator, PerkinElmer, USA) (Bartels et al., 2013). Metal-staining (here UA) of the lung tissue helped to achieve sufficient contrast, similar to previous μCT-studies of other biological tissues (Müller et al., 2017; Busse et al., 2018; De Clercq et al., 2019). The resulting overview scans could also be correlated well with histological sections.
Appendix 3—figure 1.  Illustrations of control lung tissue (hydrated).
(a) Volume rendering of the tissue block (0.97×1.00×0.73 mm3) and (b) slice through the volume, examined in PB-configuration. (c) Slice from the cone-beam scan, arrows indicating the structure of a healthy septum. Particularly, macrophages and erythrocytes emerge. Scale bars: (b) 100⁢μ⁢m and (c) 300⁢μ⁢m.
Appendix 3—figure 2.  Screening with a laboratory phase-contrast μCT-setup.
(UA-stained tissue block, patient I). (a) Histological and (b) correlative virtual slice from laboratory phase-contrast tomography. (c) Volume rendering of the entire tissue block from a similar perspective. Scale bar: 1 mm.