#Retina art or the unretina art software
Such a 1D centreline model with landmarks, visualised using viewer software allows interoperable translation to both a 2D anatomogram model and multiple 3D models of the intestines. Small and large intestines have a natural “gut coordinate” system best represented as a 1D centreline through the gut tube, reflecting functional differences. All data and software is fully open-source and available online. We also illustrate the mappings between models using a demonstrator tool that allows the user to explore the anatomical space of the gut. The outputs of this work include 1D, 2D and 3D models of the human gut, delivered through publicly accessible Json and image files. We show how locations in the 1D model can be mapped to and from points and regions in both a 2D model and 3D models, such as a patient's CT scan where the gut has been segmented.
This knowledge representation is based on a set of standardised gut anatomy ontology terms describing regions in situ, such as ileum or transverse colon, and landmarks, such as ileo-caecal valve or hepatic flexure, together with relative or absolute distance measures. Here, we focus on a Gut Linear Model (1-dimensional representation based on the centreline of the gut) that represents the location semantics as typically used by clinicians and pathologists when describing location in the gut.
We describe a conceptual coordinate model for the Gut Cell Atlas (small and large intestines). To further develop the understanding of specific pathological and histopathological phenotypes with their spatial relationships and dependencies, a more sophisticated spatial descriptive framework is required to enable integration and analysis in spatial terms. This will enable the application of bioinformatics analysis, machine learning and data mining revealing an atlas of cell types, sub-types, varying states and ultimately cellular changes related to disease conditions. The Human Cell Atlas resource will deliver single cell transcriptome data spatially organised in terms of gross anatomy, tissue location and with images of cellular histology.
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