DOI: 10.7910/dvn/nvucw8
title: Supplemented Data for: Towards automatizing detection and quantification of intestinal metaplasia: a multi-expert comparative study

description: Gastric samples from two independent cohorts. The first cohort consists of 149 asymptomatic volunteers who were selected from an independent study provided by the CIEDYN foundation, a partner of the Urkunina5000 project. This study performed an endoscopic and pathological characterization of gastric disease in 5.000 volunteers from 55 small villages in Nariño, Colombia, a region long observed as being GCa prevalent for the past two decades. Asymptomatic volunteers were men and women aged 30 − 70 years, who had lived in these areas for at least the last 10 years and had never undergone an endoscopy procedure, nor been diagnosed with GCa, any other type of cancer, or any known gastric pathology. The second cohort included 56 patients from the Hospital Universitario Nacional de Colombia included in a larger study which was approved by the ethics committee (Act No.007, Apr 29 2022). Patients were men and women who present symptoms suggestive of gastritis or other forms of gastric discomfort. However, none of them had a previous GCa diagnosis or any other type of lesion.
description: ASAP, 2.2
description: At least five gastric biopsies were obtained according to the USS in both cohorts. Specifically, two biopsies were taken from the antrum (A1, A2) (the lesser and greater curvature, both within 2 cm to 3 cm far from the pylorus), two biopsies from the corpus (C1, C2) (from the lesser curvature, approximately 4 cm proximal to the angle and from the middle portion of the greater curvature, about 8 cm from the cardias) and one biopsy from the incisura angularis (A3) (antral-corpus transition zone). All biopsies were fixed in formalin and embedded in paraffin blocks, from which successive sections from the same case were stained with H&E.

All cases were digitized using a whole-slide image (WSI) scanner (MoticEasyScan Pro), with a ×40 objective, corresponding to a spatial resolution of 0.255 μm per pixel (MPP). Each case comprised five biopsies (one per anatomical region of the stomach), resulting in a total of 205 WSI, i.e., 149 from the first cohort and 56 from the second.

Each case was independently assessed by three experienced pathologists following the Operative Link on Gastric Intestinal Metaplasia (OLGIM) system. All cases were manually annotated by the most experienced pathologist, basically delineating those regions affected by intestinal metaplasia. Overall, these regions contain not only glands with intestinal metaplasia but also a non-negligible amount of stroma and surrounding tissues.

The cases and their corresponding annotations are organized as follows:
Cases from the Urkunina5000 project (149 cases) follow the coding format UXXX, where XXX represents the case number. Cases from the Hospital Universitario Nacional de Colombia (56 cases) follow the coding format HXXX, where XXX represents the case number. The images are whole-slide images (WSI) in .svs format.

Annotations are named identically to their corresponding images to ensure proper matching. These annotations were created using the ASAP software (https://computationalpathologygroup.github.io/ASAP/) and include the following annotation types:

Numeric labels from 1 to 5 indicate glandular regions from the five anatomical regions of the stomach (1: lesser curvature of the antrum, 2: greater curvature of the antrum, 3: incisura angularis, 4: lesser curvature of the body, 5: greater curvature of the body).

The label 'IM' marks regions annotated as intestinal metaplasia.

Compressed zip files (URK_control_part_a.zip, URK_control_part_b.zip, URK_metaplasia.zip) contain 256x256 pixel image patches extracted from the annotated regions for the Urkunina5000 dataset. Similarly, the files (HUN_control_part_a.zip, HUN_control_part_b.zip, HUN_metaplasia.zip) contain corresponding patches for the Hospital Universitario Nacional de Colombia dataset.

In both datasets, control patches (without metaplasia) and metaplasia patches (intestinal metaplasia) are stored in separate folders. It is recommended to merge parts A and B of the control cases for unified analysis.