Nucleus feature profiles from GTEx histological images across 12 tissues

This dataset contains nucleus features extracted from GTEx histological images using QuPath across 12 human tissues. It also includes summary statistics of these features, which were applied in image quantitative trait loci (imageQTL) analyses and differential expression (DE) analyses. The dataset enables the exploration of relationships between nuclear morphology, genetic variation, and gene expression. By providing feature measurements across multiple tissues, it serves as a resource for integrative studies in computational pathology, imaging genomics, and functional genomics. The histological image data used in these analyses were obtained from the GTEx Portal on 10/01/2022, and we acknowledge the GTEx Consortium for providing these publicly available resources.
, QuPath v0.4.3 was used to extract nucleus features from GTEx WSIs. QuPath is publicly available (https://github.com/qupath/qupath/releases). Default settings were followed as outlined in the QuPath tutorial: https://qupath.readthedocs.io/en/stable/docs/tutorials/index.html. The image type was set to 'brightfield H&E,' and stain vectors were optimized. Subsequently, we ran a pixel classifier to identify relevant tissue areas. Cell and nucleus detection was performed using QuPath’s cell detection tool. Finally, the extracted cell and nucleus detection measurements for each WSI resulted in a structured dataset for further analysis. We configured the pipeline for each tissue type to accommodate different tissue morphologies. This automated feature extraction was crucial for ensuring consistent and objective quantification of tissue characteristics across all slides.
Four key nucleus features were included in the summary statistics: (1) nucleus area, (2) nucleus circularity, (3) nucleus ..., # Nucleus feature profiles from GTEx histological images across 12 tissues

Dataset DOI: [10.5061/dryad.8gtht771x](10.5061/dryad.8gtht771x)

## Description of the data and file structure

This dataset contains nucleus features extracted from GTEx whole-slide images (WSIs) using QuPath v0.4.3, enabling quantitative analyses of tissue morphology across multiple human tissues.

The dataset includes a total of 15 files: 12 tissue files, each corresponding to a single tissue type and stored in a compressed folder, containing nucleus feature data for individual donors derived from histological image segmentation; one summary statistics file that provides aggregated statistics across all 12 tissues; one compressed file containing differentially expressed genes for various nucleus feature groups; and one file with epigenome-wide association results linking nucleus features to methylation loci.

Key references for the dataset include QuPath ([https://github.com/qupath/qupath/releases](https://gi..., All data used in this study are derived from GTEx histological images that are publicly available on the GTEx website. These images were collected from GTEx donors under informed consent for research use. The images are fully de-identified by GTEx prior to public release, removing all personal identifiers and any information that could reasonably be used to trace back to individual donors. Our dataset contains only these de-identified, publicly accessible images and derived nucleus feature measurements, and therefore can be shared in the public domain without additional access restrictions.