Figure 6.  Tissue compactness and distance metrics: The 3D reconstructions of the lung tissue were analyzed in terms of specific surface and characteristic lengths.
The workflow is sketched for sample V in the top part (a–g). In a first step, the tissue was segmented using Ilastik. A slice of the reconstructed electron density is shown in (a). Based on the segmentation, the areas of air which are directly connected and potentially filled with oxygen (or blood) are masked out (b). (c) For each of the remaining tissue voxels the shortest possible distance to air was calculated. Especially around vessels and larger alveoli, the distances are larger. (d) Zoom into an area around a vessel. Further analysis is based on the distance distribution shown in (e). (f) Volume rendering of the reconstructed electron density, with (g) showing the corresponding 3D distance map. (h) Based on the tissue segmentation of all samples, the distance from the tissue interior to the closest air compartment was calculated. In order to compare all samples, the count of voxels was normalized by the total volume of the respective sample. The specific surface area SV (represented by the first value of each curve), the characteristic length Lc and the mean distance dO2¯ for each sample was calculated based on this data. Double logarithmic scale, bin width of the distribution of distances: 1 v⁢x. Scale bars: (a–c) 100⁢μ⁢m.