Img2ST-Net: Efficient High-Resolution Spatial Omics Prediction from Whole Slide Histology Images via Fully Convolutional Image-to-Image Learning

TL;DR

Img2ST-Net introduces a fully convolutional, parallelized framework for high-resolution spatial transcriptomics prediction from histology images, addressing computational challenges and improving spatial accuracy.

Contribution

The paper presents a novel super-pixel based, fully convolutional model for efficient high-resolution spatial transcriptomics prediction from histology images, with a new evaluation metric.

Findings

Improved computational efficiency over traditional methods.

Enhanced spatial organization preservation in predictions.

Robust performance on high-resolution spatial transcriptomics data.

Abstract

Recent advances in multi-modal AI have demonstrated promising potential for generating the currently expensive spatial transcriptomics (ST) data directly from routine histology images, offering a means to reduce the high cost and time-intensive nature of ST data acquisition. However, the increasing resolution of ST, particularly with platforms such as Visium HD achieving 8um or finer, introduces significant computational and modeling challenges. Conventional spot-by-spot sequential regression frameworks become inefficient and unstable at this scale, while the inherent extreme sparsity and low expression levels of high-resolution ST further complicate both prediction and evaluation. To address these limitations, we propose Img2ST-Net, a novel histology-to-ST generation framework for efficient and parallel high-resolution ST prediction. Unlike conventional spot-by-spot inference methods, Img2ST-Net employs a fully convolutional architecture to generate dense, HD gene expression maps in a parallelized manner. By modeling HD ST data as super-pixel representations, the task is reformulated from image-to-omics inference into a super-content image generation problem with hundreds or thousands of output channels. This design not only improves computational efficiency but also better preserves the spatial organization intrinsic to spatial omics data. To enhance robustness under sparse expression patterns, we further introduce SSIM-ST, a structural-similarity-based evaluation metric tailored for high-resolution ST analysis. We present a scalable, biologically coherent framework for high-resolution ST prediction. Img2ST-Net offers a principled solution for efficient and accurate ST inference at scale. Our contributions lay the groundwork for next-generation ST modeling that is robust and resolution-aware. The source code has been made publicly available at https://github.com/hrlblab/Img2ST-Net.