The Human Gut Cell Atlas Project comprises a multi-disciplinary group covering all aspects of the work from the clinical assessment and tissue collection through processing, analysis and data-publication including the conceptual model development and realization via online tools and annotation standards. The effort is part of the wider Helmsley Crohn’s disease and Human Cell Atlas programmes and therefore includes engagement and collaboration with the wider community especially in the development of standards and protocols for data collection and integration. Clinical Protocols, Standards and Procedures Protocols and standards used for tissue collection, tissue processing, radiological imaging and experimental design. Tissue Processing, Histopathology Imaging and Single Cell Sequencing Protocols and standards used f for histopathology processing, imaging and single-cell sequencing. Comparative Pathology Workbench The Comparative Pathology Workbench for image and atlas data including scRNA-Seq and pathology analysis. Edinburgh Gut Cell Atlas and Common Coordinate Framework The 1D-, 2D- and 3D-Gut Models and the GCA Common Coordinate Framework Analysis, Data-Management and Data-Publication scRNA-Seq Analysis, Data-Management and Data-Publication This article was published on 2024-08-27