JADE: Joint Alignment and Deep Embedding for Multi-Slice Spatial Transcriptomics.

ABSTRACT: As spatially resolved transcriptomics (SRT) datasets increasingly span multiple adjacent or replicated slices, effective joint analysis across slices is needed to reconstruct tissue structures and identify consistent spatial gene expression patterns. This requires resolving spatial correspondences between slices while capturing shared transcriptomic features, two tasks that are typically addressed in isolation. Multi-slice analysis remains challenging due to physical distortions, technical variability, and batch effects. To address these challenges, we introduce Joint Alignment and Deep Embedding for multi-slice SRT (JADE), a unified computational framework that simultaneously learns spatial location-wise alignments and shared low-dimensional embeddings across tissue slices. Unlike existin

SUBMITTER: Guo Y 

PROVIDER: S-EPMC12699533 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature