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Pediatric inflammatory bowel disease (IBD) Description
The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.

Technical details
Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.

CHOC Research Institute - Children’s Hospital of Orange County

Dataset contact: Chloe Martin-King (chloe.martin.king@choc.org)

View images by patient number
Patient 1
Patient 2
Patient 3
Patient 4

Patient 5
Patient 7
Patient 9
Patient 10

Patient 11
Patient 13
Patient 14
Patient 17

Patient 18
Patient 19
Patient 20
Patient 21

Patient 22
Patient 23

Licensing
Attribution Only: This image is licensed under a Creative Commons Attribution License. View License Deed | View Legal Code

Instructions for downloading the CHOC IBD dataset
1) To download the entire dataset, use the PHP file provided at https://github.com/CRBS/CIL_RS/wiki/Download_CHOC_dataset

2) Each image .tif file will be downloaded to a zip file. The .tif image files are named according to the metadata in the excel linked below. This way, once the images are extracted from the zip files, they can be linked to patient and scan attributes.

3) The labels and data dictionary can be found in the excel file at Pediatric_IBD_StructuredData.xlsx