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Spatially resolved omics technologies are transforming our understanding of biological tissues. However, the handling of uni- and multimodal spatial omics datasets remains a challenge owing to large data volumes, heterogeneity of data types and the lack of flexible, spatially aware data structures. Here we introduce SpatialData, a framework that establishes a unified and extensible multiplatform file-format, lazy representation of larger-than-memory data, transformations and alignment to common coordinate systems. SpatialData facilitates spatial annotations and cross-modal aggregation and analysis, the utility of which is illustrated in the context of multiple vignettes, including integrative analysis on a multimodal Xenium and Visium breast cancer study., Competing Interests: Competing interests: J.M. holds equity in Glencoe Software, which builds products based on OME–NGFF. F.J.T. consults for Immunai, Inc., Singularity Bio B.V., CytoReason Ltd, Cellarity and Omniscope and has ownership interest in Dermagnostix GmbH and Cellarity. O.S. is a paid consultant of Insitro, Inc., S.K.S. is a consulting scientific cofounder for Digital Biology, Inc. The remaining authors declare no competing interests., (© 2024. The Author(s).)

Inflammatory bowel disease (IBD) patients may bear an increased neuroendocrine tumor (NET) risk. These tumors are mostly reported as coincidental findings during surgery. We aimed to determine the prevalence of colonic NET in a Dutch nationwide IBD cohort and calculate the prevalence rate ratios (PRR) compared with the general Dutch population. Our second aim was to investigate whether a high bowel surgery rate in IBD could result in a high PRR for NET. The Dutch Pathology Registry (PALGA) was searched to identify all IBD patients with colonic NET in The Netherlands between 1991 and 2011. We determined the prevalence and PRR of colonic NET in a 20-year period. For our second aim, we compared NET prevalence in colonic resection specimens between IBD cases and non-IBD controls (diverticulitis and ischemia). We identified 51 IBD patients who developed colonic NET resulting in a prevalence of 60.4-89.3 per 100,000 patients in a 20-year period with a PRR of 2.8-4.1. However, adjusted for resection type, sex and age, a higher NET prevalence was shown in diverticulitis (OR 5.52, 95% CI 3.47-8.78) and ischemia (OR 1.97, 95% CI 1.09-3.58) compared with IBD. Our key finding is that NET are more prevalent in IBD patients compared with the general population (PRR 2.8-4.1). This might be attributed to a high rate of incidental NET as IBD patients frequently undergo intestinal surgery. A lower adjusted NET prevalence in colonic resection specimens for IBD compared to ischemia and diverticulitis supports this hypothesis., (© 2016 UICC.)