LitCovid-sentences  

PMC:7473770 / 40941-43850 JSONTXT 9 Projects

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Id Subject Object Predicate Lexical cue
T318 0-37 Sentence denotes Image segmentation and quantification
T319 38-139 Sentence denotes For each patient the stitched overview scans were analyzed with regard to structural characteristics.
T320 140-362 Sentence denotes The 3D-reconstructions were first binned (2 × 2 × 2), and the tissue was then segmented from the surrounding paraffin using the segmentation software Ilastik (Berg et al., 2019), which was then further refined with MATLAB.
T321 363-501 Sentence denotes In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map.
T322 502-617 Sentence denotes Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block.
T323 618-713 Sentence denotes Individual self-contained areas of paraffin (not connected to air) were excluded from the mask.
T324 714-831 Sentence denotes Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel.
T325 832-904 Sentence denotes The tissue volume V is given by the sum of all voxels containing tissue.
T326 905-995 Sentence denotes The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air.
T327 996-1101 Sentence denotes From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio.
T328 1102-1210 Sentence denotes Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample.
T329 1211-1346 Sentence denotes Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated.
T330 1347-1485 Sentence denotes Hyaline membranes and capillary networks were extracted using semi-manual segmentation functions in Avizo (Thermo Fisher Scientific, USA).
T331 1486-1641 Sentence denotes Beside hyaline membranes and the capillary network, different cell types can be readily identified based on the 3D reconstructions of the electron density.
T332 1642-1752 Sentence denotes In particular, inflammatory cell subpopulations - that is, macrophages and lymphocytes - can be distinguished.
T333 1753-1866 Sentence denotes To this end, an automatic and parameter-controlled algorithm denoted as BlobFinder was used (arivis AG, Germany).
T334 1867-2010 Sentence denotes Based on its segmentation output, the amount and position of the lymphocytes in the 3D-reconstructions from parallel beam scans was calculated.
T335 2011-2083 Sentence denotes The algorithm is able to identify roundish structures with a given size.
T336 2084-2167 Sentence denotes For the segmentation of the lymphocytes, we chose a characteristic size of 6.5⁢μ⁢m.
T337 2168-2266 Sentence denotes The structures identified in this step also include macrophages and parts of the capillary system.
T338 2267-2415 Sentence denotes For the unbinned datasets, a distinction between lymphocytes and the nuclei of the macrophages was made based on the difference in electron density.
T339 2416-2524 Sentence denotes In the tomographic reconstructions, the lymphocytes appear denser compared to the nuclei of the macrophages.
T340 2525-2665 Sentence denotes Further, nuclei from endothelial cells and parts of the capillaries filled with blood residues were excluded based on their elongated shape.
T341 2666-2731 Sentence denotes Only structures with a sphericity higher than 0.55 were included.
T342 2732-2909 Sentence denotes 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 estimated.