H&Enium
H&Enium is a curated single-cell dataset linking H&E histology images with spatial transcriptomic measurements and cell-type annotations from paired Xenium samples.
The dataset is currently being prepared for public release.
Dataset overview
H&Enium contains millions of spatially registered cells derived from paired H&E and Xenium data. Each cell is associated with:
- H&E image information
- Spatial coordinates
- Gene expression measurements
- Curated cell-type annotations
- Sample and tissue metadata
The dataset is designed to support development and benchmarking of computational pathology models at single-cell resolution, including:
- Cell-type classification from H&E
- Gene-expression prediction from morphology
- Evaluation of pathology foundation models
- Multimodal H&E–transcriptomics representation learning
Data sources
Samples are derived from publicly available spatial transcriptomics datasets, including data collected through the HEST-1k resource. Cells are spatially registered between H&E images and Xenium measurements and subsequently processed through a multi-stage annotation pipeline.
Availability
🚧 Dataset release in preparation
The complete curated dataset will be made publicly available following publication of the associated work.
This repository will serve as the main distribution point for the dataset.
Citation
Citation information will be added upon publication.
Contact
For questions regarding the dataset or early access discussions, please contact marcchristian.glettig@inf.ethz.ch of the associated study.
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