HEST-1k: 用于空间转录组和组织学图像分析的数据集
摘要
空间转录组技术使人类能够不断提高对组织分子组成的解析分辨率和灵敏度。然而, due to costs, rapidly evolving technology, and lack of standards, computational methods in ST have been constrained to narrow tasks and small cohorts. 此外, the underlying tissue morphology, as reflected by H&E-stained whole slide images (WSIs), encodes rich information often overlooked in ST studies. 因此, 我们介绍 HEST-1k, a collection of 1,229 spatial transcriptomic profiles, each linked to a WSI and extensive metadata. HEST-1k was assembled from 153 public and internal cohorts encompassing 26 organs, two species (Homo Sapiens and Mus Musculus), and 367 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 2.1 million expression--morphology pairs and over 76 million nuclei. To support its development, we additionally introduce the HEST-Library, a Python package designed to perform a range of actions with HEST samples. We test HEST-1k and Library on three use cases: (1) benchmarking foundation models for pathology (HEST-Benchmark), (2) biomarker exploration, (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed at https://github.com/mahmoodlab/hest.
引用
@article{arxiv.2406.16192,
title = {HEST-1k: A Dataset for Spatial Transcriptomics and Histology Image Analysis},
author = {Guillaume Jaume and Paul Doucet and Andrew H. Song and Ming Y. Lu and Cristina Almagro-Pérez and Sophia J. Wagner and Anurag J. Vaidya and Richard J. Chen and Drew F. K. Williamson and Ahrong Kim and Faisal Mahmood},
journal= {arXiv preprint arXiv:2406.16192},
year = {2024}
}
备注
NeurIPS'24 Spotlight