PMC:7473770 / 42288-43850
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":"Hyaline membranes and capillary networks were extracted using semi-manual segmentation functions in Avizo (Thermo Fisher Scientific, USA). Beside hyaline membranes and the capillary network, different cell types can be readily identified based on the 3D reconstructions of the electron density. In particular, inflammatory cell subpopulations - that is, macrophages and lymphocytes - can be distinguished. To this end, an automatic and parameter-controlled algorithm denoted as BlobFinder was used (arivis AG, Germany). Based on its segmentation output, the amount and position of the lymphocytes in the 3D-reconstructions from parallel beam scans was calculated. The algorithm is able to identify roundish structures with a given size. For the segmentation of the lymphocytes, we chose a characteristic size of 6.5μm. The structures identified in this step also include macrophages and parts of the capillary system. For the unbinned datasets, a distinction between lymphocytes and the nuclei of the macrophages was made based on the difference in electron density. In the tomographic reconstructions, the lymphocytes appear denser compared to the nuclei of the macrophages. Further, nuclei from endothelial cells and parts of the capillaries filled with blood residues were excluded based on their elongated shape. Only structures with a sphericity higher than 0.55 were included. Based on the segmentation of lymphocytes, the total number of lymphocytes Nl was obtained and the mean concentration of lymphocytes within the lung tissue cl=Nl/V was 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