*2.11. Image Analyses and 3D Reconstructions*

In order to provide an unbiased and quantitative description of histological slices, a problemspecific image analysis pipeline was developed. Depending on the utilized staining and after performing necessary preprocessing, various related features were segmented. These segmentations were verified by domain knowledge experts, serving as a gold standard. Subsequent measurements were then performed before producing the final summary statistic. Both ImageJ [36] and Matlab R2019a were utilized throughout the quantification process. The former was used for exploration and the later for developing dedicated programs. In the case of bright field scans and after obtaining satisfactory segmentation of a CYP-positive area as well as the associated corresponding background, a ratio was recorded. For the 3D reconstruction, individual structures (nuclei, CYP-positive area and the vessels) were also first segmented and verified. The final reconstruction and visualization were prepared using Imaris 9.3 software.
