Published April 30, 2025
| Version v1
Dataset
Open
Atlas of Digital Pathology v2 — Part I
Creators
- Yang, Zhiyuan (Researcher)1
- Li, Kai (Researcher)2
- Ramandi, Sophia Ghamoshi (Annotator)3
- Brassard, Patricia (Researcher)4
- Khellaf, Hakim (Researcher)4
-
Trinh, Vincent Quoc-Huy
(Researcher)4, 5
- Zhang, Jennifer (Researcher)2
- Chen, Lina (Researcher)6, 2
-
Rowsell, Corwyn
(Researcher)7
-
Varma, Sonal
(Researcher)8
-
Plataniotis, Konstantinos
(Supervisor)2
- Hosseini, Mahdi S. (Supervisor)1
-
1.
Concordia University
-
2.
University of Toronto
-
3.
Toronto Metropolitan University
-
4.
Université de Montréal
-
5.
Centre Hospitalier de l'Université de Montréal
-
6.
Sunnybrook Health Science Centre
- 7. Unity Health Toronto
-
8.
Queen's University
Description
- This is the first part (1/3) of the Atlas of Digital Pathology v2 (ADPv2) dataset, featuring 20k non-overlapping image patches from hematoxylin & eosin (H&E) and hematoxylin phloxine saffron (HPS) stained histological images of healthy colon tissue
- Parts (2/3) and (3/3) can be found here: ADPv2 Part (2/3) , ADPv2 Part (3/3)
- Contains zip files 1 through 12, each of which containing 1000 image patches. Annotations and metadatas attached as separate csvs.
- All images have a FOV of 544x544 microns, or 1360x1360 pixels (px) at 0.4 mpp (20x).
- Tissue classes are as follows: Surface Epithelium (SE), Stratified Squamous (SS), Nonkeratinized Squamous Mucosa (NSM), Keratinized Squamous Epithelium (anal skin) (KSE), Simple Columnar (SCL), Foveolar (stomach) (F), Small Bowel (VESGC), Large Bowel (BBNGC), Glands (GD), Glandular (GL), Small Bowel Cryps (SBC), Large Bowel Crypts (LBC), Mucous Glands (MG), Esophageal Mucous Glands (EMG), Anal Mucous Glands (AMG), Lamina Propria (LP), Lymphoid Aggregates (LA), Lymphovascular Channels (LC), Smooth Muscle Cells (SMC), Elastic Fibers (EF), Neural Tissue (NT), Nerve Fiber (NF), Ganglion Cells (GC), Connective Tissue (CT), Inflammatory Cells (IC), Polymorphonuclear Cells (POC), Neutrophils (NTR), Eosinophils (ES), Mononuclear Cells (MOC), Macrophages (MA), Plasma Cells (PC), Lymphocytes (LY), Red Blood Cells (RBC), Vessels (V), Adipose Tissue (AT), Mesothelial Cells (MC)
- The whole slide images (WSIs) used in this project originate from multiple sources, including "The Cancer Genome Atlas (TCGA)" provided by the National Cancer Institute (NCI); Kingston General Hospital (KGH;
Canada), St. Michael’s Hospital (SMH; Canada), and Sunnybrook Research
Institute (SRI; Canada). Each slide used in our project is derived from healthy colon biopsies. In total, there are 461 slides. See a detailed breakdown below:- 200 KGH slides, having 20x magnification, 0.4 mpp, and HPS staining
- 110 TCGA slides, having 20x magnification, 0.5 mpp, and H&E staining
- 131 SMH slides, having 50x magnification, 0.2 mpp, and H&E staining
- 20 SRI slides, having 40x magnification, 0.25 mpp, and H&E staining
- When using this resource, please cite our original paper: ADPv2: A Hierarchical Histological Tissue Type-Annotated Dataset for Potential Biomarker Discovery of Colorectal Disease
Files
colon_annotations_batch_1.csv
Files
(44.0 GB)
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Additional details
Software
- Development Status
- Active