140 HE and 111 CD3-stained colon biopsies of active and inactivate inflammatory bowel disease with epithelium annotated: the IBDColEpi dataset

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General description and ethics approvals: The dataset contains 140 HE and 111 CD3 stained, formalin fixed paraffin embedded (FFPE) biopsies of colonic mucosa. The biopsies were extracted from the NTNU/St. Olavs hospital, Trondheim University Hospital (Norway) biobank of patients with confirmed inflammatory bowel disease or healthy controls with gastrointestinal symptoms but no macroscopic- or microscopic disease. Inclusion and colonoscopies were performed at the Department of Gastroenterology and Hepatology at St. Olavs hospital, Trondheim University Hospital from 2007 to 2018. All patients gave written informed consent and ethical approvals were obtained from the Central Norway Regional Committee for Medical and Health Research Ethics (reference number 2013/212/REKMidt). Consent to publish the anonymized whole slide image (WSI) dataset was given by REKMidt in 2021. Each database ID number used in this study was changed to new anonymized IDs only containing the information “active” or “inactive” disease and whether the WSI has haematoxylin-eosin (HE) staining or CD3 immunostaining. The biopsies included in the biobank are sampled such that one biopsy from an unaffected/inactive area and one from an area affected/active area were included from each patient and given a separate ID number. Hence, two biopsies with different ID numbers can be from the same patient. "Active" is defined as the presence of intraepithelial granulocytes in one or more location in the biopsies. Still, the changes may be focal, hence majority of the epithelium may still lack intraepithelial granulocytes or other signs of active disease (crypt abscesses, granulation tissue, etc.).

Annotation procedures: While annotating epithelium, we strived to draw lines as close to the basement membrane as possible where visible. All annotations were finally refined by the following QuPath scripts to ensure consistency throughout the datasets: - Minimum fragment size min 75 um^2 - Minimum hole size min 100 um^2 - remove white background with intensity greater than 220 average all channels with sigma 2.5 - expand and shrink all annotations 1.0 mm.

Laboratory methods: FFPE sections of 4 µm were cut, mounted on slides and either stained with hematoxylin (Mayer’s) and Eosin (Y) (HE) or subjected to standard pre-treatment with quenching of endogenous peroxidase and boiling in Tris EDTA pH9 for antigen retrieval before immunohistochemistry. Primary antibody for the T lymphocyte marker was mouse anti-human CD3 (M7254, clone F7.2.38, Dako Agilent, CA, USA), diluted 1:50 in antibody diluent Tris buffer with 0.025% Tween-20 and 1% BSA and incubated overnight at 4 °C. Immunoreactions were visualized with the secondary antibody rabbit/mouse EnVisionHRP/DAB+ kit (K5007, Dako Agilent) and counterstaining with haematoxylin. Omission of the primary antibody was used as negative control and sections from human peripheral lymph node as positive control.