BASSL-MI: Batch-Agnostic Self-Supervised Learning Uncovers Clinically Relevant Tumor Niches in Multiplexed Imaging

ABSTRACT Multiplexed imaging enables rich, high-resolution characterization of the tumor microenvironment but relies on labor-intensive and error-prone cell segmentation and phenotyping pipelines. We present BASSL-MI, a batch-agnostic, self-supervised framework for discovering tissue niches directly from multiplexed imaging data. BASSL-MI operates directly on image patches, eliminating the need for explicit cell segmentation while mitigating image-, sample-, or batch-specific artifacts. Built on a modified contrastive block disentanglement architecture, BASSL-MI learns dual latent representations that separate biologically informative features from batch-dependent factors through spatially guided augmentations and batch-invariance objectives. Applied to a 56-marker colorectal cancer CODEX dataset, BASSL-MI-trained embeddings markedly reduce image-specific variability and recover biologically interpretable spatial niches. Notably, it uncovers CD20–rich follicular regions associated with improved survival, outperforming published findings from cell segmentation-driven clustering. This work demonstrates that self-supervised, patch-based learning can capture clinically relevant spatial organization within tumor microenvironments, advancing toward automated, non-cell-based analysis of multiplexed imaging data.