Statistical batch-aware embedded integration, dimension reduction and alignment for spatial transcriptomics

Spatial transcriptomics (ST) technologies provide richer insights into the molecular characteristics of cells by simultaneously measuring gene expression profiles and their relative locations. However, each slice can only contain limited biological variation, and since there are almost always non-negligible batch effects across different slices, integrating numerous slices to account for batch effects and locations is not straightforward. Here, we propose a hierar-chical hidden Markov random field model STADIA to reduce batch effects, extract common biological patterns across multiple ST slices, and simultaneously identify spatial domains. We demonstrate the effectiveness of STADIA using five datasets from different species (human and mouse), various organs (brain, skin, and liver), and diverse platforms (10x Visium, ST, and Slice-seqV2). STADIA can capture common tissue structures across multiple slices and preserve slice-specific biological signals. In addition, STADIA outperforms the other three competing methods (PRECAST, fastMNN and Harmony) in terms of the balance between batch mixing and spatial domain identification.