RendeiroLab/histomorphological-cell-atlas

Histomorphological Atlas of Single Cells across the Human Life Span

A billion-scale single-cell atlas of human tissue from whole-slide histopathology images across 16 organs. This dataset contains cell type densities (cells per mm²), spatial coordinates, morphological phenotypes, and tissue graphs derived from deep learning analysis of H&E-stained tissue sections from 980 donors (ages 20-70) in the GTEx cohort.

Dataset Description

We applied deep learning to 14,788 whole-slide H&E images from the GTEx project, detecting and classifying over 3.5 billion single cells. This dataset provides the processed outputs of that pipeline, including per-slide cell type densities, per-cell spatial coordinates, cell type identities, and slide-level tissue graphs.

Organs Covered

16 organs (20 tissue subtypes): Adrenal Gland, Colon (Sigmoid, Transverse), Esophagus (Gastroesophageal Junction, Mucosa, Muscularis), Liver, Lung, Ovary, Pancreas, Prostate, Skin (Sun-Exposed, Not Sun-Exposed), Small Intestine (Terminal Ileum), Spleen, Stomach, Testis, Thyroid, Uterus, Vagina.

Contents

File	Description
16_tissues_cell_abundances.parquet	Cell type densities (cells per mm²) across all 16 tissues, collapsed by cell phenotype
(forthcoming) Cell polygons	Per-cell spatial polygon coordinates for each slide
(forthcoming) Cell identities	Per-cell type classification for each slide
(forthcoming) Slide graphs	Tissue-level spatial graphs for each slide

Data Format

16_tissues_cell_abundances.parquet

Columns:

• slide_id: GTEx slide identifier
• organ: Organ/tissue name
• mpp: Microns per pixel (image resolution)
• pixels: Total pixel area analyzed
• cells_pmm2: Total cell density (cells per mm²)
• endothelial_error_pmm2: Endothelial segmentation error density (cells per mm²)
• Remaining columns: Cell phenotype densities (cells per mm²) — including Hepatocyte/Chromaffin, Connective, Immune, Cuboidal, Muscle, Glandular, Elongated, Glandular (Columnar), Epithelial, Dead, Endothelial, Squamous, Alveolar, Seminiferous, Follicular

Source Data

Whole-slide images and metadata from the GTEx project:

• GTEx Histology Portal
• GTEx Sampling Site Page

GTEx whole-slide images are publicly available from the GTEx portal. Associated donor metadata and transcriptomic data are available through dbGaP under controlled access.

Pipeline Summary

Cells were segmented and classified from whole-slide H&E images using CellViT (SAM-H backbone). Cell phenotyping integrates CellViT morphological features and DINOv2 (ViT-S/14) nuclear features, with PLIP providing text-based guidance, to classify each cell into a phenotype class.

Citation

If you use this dataset, please cite:

Abila, E., Zheng, Y., Bago-Horvath, Z. & Rendeiro, A.F. A single-cell view of human
tissue aging reveals architectural decline beyond cellular composition. (2026).

License

This dataset is licensed under CC-BY-NC-ND-4.0.

Contact

Andre F. Rendeiro — arendeiro@cemm.oeaw.ac.at