Figure 1

Example workflow illustrating the acquisition and processing of FTU data from a three-dimensional reconstruction of human colon tissue. Step 1: The FTU template (A) is prepared according to the biophysical constraints under consideration, such that the long axis of the resulting cylindrical block of tissue is that of the feeding capillary (CAP) on which it is metabolically dependent. This template is applied to an appropriate volumetric region in the three-dimensional histology image dataset (B). The various cells within this region (coloured boxes) are typed and their position recorded (Note: red boxes represent endothelial cells, here shown lining the feeding capillary – CAP – and the erythrocytes within its lumen). Step 2: The cellular annotations across the full extent of the FTU cylindrical boundaries (C) are stored, together with the image data and the anatomical provenance of the tissue sample. Step 3: As the resulting primary tissue motif for the above colonic FTU uses standard reference ontology terms to represent both (i) a non-redundant list of distinct cell types, as well as (ii) the anatomical region of origin for the sourced tissue material, a terse graphical depiction of the constitution of this FTU may be automatically included in the context of whole-body anatomy maps, such as the one schematized by the ApiNATOMY tool[9] in (D). In this schematic, the outer boundary of the map represents the various epithelial surface categories (each individually coloured and labelled), and the inside tiles represent vascular (red) and neural (purple) structures respectively.