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{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T13","span":{"begin":2451,"end":2460},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T14","span":{"begin":2892,"end":2904},"obj":"http://purl.obolibrary.org/obo/GO_0006954"},{"id":"T15","span":{"begin":5735,"end":5747},"obj":"http://purl.obolibrary.org/obo/GO_0006954"},{"id":"T16","span":{"begin":6385,"end":6395},"obj":"http://purl.obolibrary.org/obo/GO_0036074"},{"id":"T17","span":{"begin":6519,"end":6531},"obj":"http://purl.obolibrary.org/obo/GO_0006954"}],"text":"Reconstructed electron density\nNext, we present representative slices through the reconstruction volumes of all samples for all acquisition scales. Figure 3 presents the stitched reconstruction volumes, recorded under conditions of local tomography, see Table 3. Conventional HE-stained histology images of all samples are shown in Appendix 1—figure 1. Since these volumes are computed from stitching up to 20 individual tomograms, the question arises to which extend the image quality is limited by potential artifacts of local tomography, that is, errors due to the fact that part of the sample is outside the reconstruction volume. For this reason, 1 mm punches were taken after the stitched overview and rescanned in the parallel beam configuration, without local tomography conditions, since they fitted within the FOV. The results are presented in Figure 4, and validate the previous stitching results. The 1 mm punches then also provided an appropriate size for the cone-beam recordings, which are shown in Figure 5. Importantly, in each scan the previous level guided the choice for the next FOV and informed about the larger environment. In the following, we briefly discuss the samples one-by-one, with regard to all acquisition scales. A comparison of morphological features between conventional and virtual histology is shown in the Appendix 1.\nFigure 3. Stitched parallel-beam reconstructions for full pulmonary samples (I–VI).\nRepresentative virtual sections through the reconstruction volumes of full biopsies (I–VI), respectively. Scale bars: 500⁢μ⁢m.\nFigure 4. Parallel-beam reconstructions for 1 mm biopsy punches (I–VI).\nRepresentative virtual sections through the reconstruction volumes of the 1 mm punches into the volumes of the full biopsies (I–VI), respectively. The fact that the punches are isolated results in higher image quality, since the errors associated with local tomography are avoided. Scale bars: 100⁢μ⁢m.\nFigure 5. Cone-beam reconstructions for biopsy punches (I–VI), shown for approximately the same slices as in Figure 4 for the parallel beam reconstruction.\nVirtual sections through the reconstruction volumes of the cone-beam recordings corresponding to sections in Figure 4, obtained by the parallel beam configuration, for biopsies (I–VI) , respectively. Scale bars: 100⁢μ⁢m.\n\nSample I\nBy conventional histopathological assessment, the peribronchial alveolar parenchyma of sample I showed DAD with focal formation of hyaline membranes adjacent to the epithelial lining, moderate lymphocytic interstitial pneumonia and singular thrombi in small pulmonary veins. There is a moderate hypertrophy of the muscular media in smaller pre- and post-capillary blood vessels with desquamation of the endothelial cell layer as well as mild centrilobular emphysema (original magnification 100×). In PC-CT, enlarged alveolar septa with pronounced lymphocytic inflammation are displayed. The reconstruction volume contains a large artery filled with erythrocytes (Figure 3-I, lower left), which bifurcates into two vessels. This area was then selected for the 1 mm biopsy punch extraction. The cone-beam zoom tomogram was then centered around the perimeter of the blood vessel. This volume is particularly well suited to investigate the connective tissue including elastic fibers and collagen, as well as smooth muscle.\n\nSample II\nHistomorphological analysis shows peribronchial alveolar parenchyma with hyperemia of capillary and post-capillary blood vessels, as well as a moderate centrilobular emphysema (original magnification 100×). On the level of blood vessels, both blood-filled and empty vessels are discernible. It should be noted that septa with signs of parallel capillaries are visible. In the reconstruction volume of the zoom tomogram, a single vessel can be easily tracked over large distances.\n\nSample III\nThe sample consists of peribronchial alveolar parenchyma showing prominent multifocal neutrophilic capillaritis as well as a moderate centrilobular emphysema (original magnification 100×). In PC-CT, septa with again similar physiological size and distribution emerge, with moderate emphysema. The bottom part of the sample contains a fibrous area near a larger blood vessel. The zoom tomogram shows a single septum, a blood vessel and a fibrous region.\n\nSample IV\nHistomorphological analysis shows peribronchial alveolar parenchyma with marked lymphocytic interstitial pneumonia, multifocal venous thrombi and focal intraalveolar fibrin deposition in terms of DAD. Furthermore, there is a mild centrilobular emphysema (original magnification 100×). In PC-CT, a network of thin septa, thrombi and emphysema, as well as a large empty blood vessel appears. Electron-rich diffuse black granules are also visible. The biopsy punch was selected to contain the empty blood vessel, some small thrombi. It also includes thin septa and tissue embedded dirt-particles. The zoom tomogram covered tissue with black granules as well as a band of inflammatory cells next to a septum wall.\n\nSample V\nBy conventional histological assessment, Sample V consists of peribronchial alveolar parenchyma showing massive lymphocytic interstitial pneumonia with ubiquitous hyaline membranes superimposed on the alveolar walls, neutrophilic capillaritis and multifocal post-capillary thrombi in terms of severe DAD. Furthermore, bronchialized alveolar epithelial cells show cytopathic changes and multifocal desquamation, as does alveolar macrophages. Focally, accumulation of intraalveolar neutrophilic granulocytes in the sense of a florid bronchopneumonia can be observed (original magnification 100×). PC-CT data give rise to alterations of the overall morphology due to Covid-19, including substantial inflammation, pronounced hyaline membranes, and high load of lymphocytes. The biopsy punch was chosen to include areas with increased presence of hyaline membrane and lymphocytes. A blood vessel splitting into several smaller blood vessels is easily recognized when browsing through the reconstructed volume. Noteworthy, different cell types as macrophages, T-cells or erythrocytes can be distinguished in the zoom tomogram.\n\nSample VI\nHistomorphological analysis shows peribronchial alveolar parenchyma with lymphocytic interstitial pneumonitis and a singular thrombus in a small vein. The interstitium of the alveolar septae is widened by myogenic metaplasia. Adjacent, centrilobular emphysema and anthracosis are observed. The bronchial mucosa shows varying degrees of lymphocytic inflammation in the sense of chronic bronchitis/bronchiolitis (original magnification 100×). From PC-CT reconstructions, the sample consists of thin alveoli (Figure 3VI, upper left) evolving into compact, fibrotic tissue (Figure 3VI, lower right). The amount of lymphocytes is rather low in this sample. Black granules and some thrombi are embedded within the bulky tissue parts. The biopsy punch covers the region of transition from alveoli to fibrotic tissue, containing also a thrombus and capillaries as identified from the zoom tomogram."}

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