Room-temperature SEM array tomography of TIFF CDMs grown for 14 days. (A) Four exemplary 70 nm thick sections from different z-height positions within the CDM are shown. (B) The same slices shown in A were segmented for nuclei, cytoplasm, and ECM using Ilastik (Berg et al., 2019) and are colored as indicated. (C) 3D segmentation of an exemplary cell embedded within the CDM (denoted by a black asterisk in A), shown in a top (left) and oblique view (middle). On the right side, an ortho-slice view of the same cell is shown, highlighting the thin z-height of the cell embedded within the ECM. Please note that the other cells in the vicinity of the segmented cell have been omitted from this view to facilitate visualization. Color code of the segmentation is indicated below. (D) The directionality of cells and fibers is color-coded as indicated on the right, corresponding to the angles of cells and fibers. The same z-positions as shown in A are depicted to show the change in directionality throughout the height of the CDM. Scale bar dimensions are annotated in the figure.