Faisal Mahmood: Meet HEST-1k, a collection of 1,108 ST samples

Faisal Mahmood, Associate Professor at Harvard University, shared on X:

“What would you do with 1000+ spatial transcriptomics samples with corresponding H and E-stained whole-slide images? Meet HEST-1k, a collection of 1,108 ST samples assembled from 131 public and internal cohorts encompassing 25 organs, 2 species. HEST-1k includes over 1.5 million expression–morphology pairs.

Explore 3 use-cases for HEST-1k: – HEST-Benchmark: Evaluate gene expression prediction from histology across 10 organs and 9 cancer types, testing multiple foundation models for pathology including UNI, and GigaPath. – HEST for discovery: Explore our proof-of-concept for multimodal biomarker characterization using Xenium breast cancer samples. – HEST for fine-tuning pathology foundation models: See how HEST-1k can enhance foundation models for histology with expression-guided fine-tuning..

Preprint.
Code and Data access.

Congratulations to Guillaume Jaume, Paul Doucet, and everyone else who contributed to this work. Huge thanks to everyone who helped curate the dataset. ”

Source: Faisal Mahmood/X