A multiperspective evaluation framework of spatial transcriptomics clustering methods

Spatial transcriptomics (ST) allows the exploration of gene expression within tissue microenvironments, driving the development of multiple computational approaches for spatial domain identification. Evaluating these methods typically relies on label-dependent metrics, such as contingency matrices and information-theoretic measures, which require ground-truth annotations, and label-independent metrics, which assess transcriptomic similarity or spatial organization. However, annotations are often incomplete or unavailable, while label-independent metrics fail to jointly evaluate the integration of transcriptomic and spatial information, a core feature of ST clustering methods. To address these limitations, we introduce MultimetricST, a Python-based framework that provides a unified, flexible evaluation strategy integrating both cutting-edge and state-of-the-art label-dependent and label-independent metrics. We applied MultimetricST on two generated synthetic datasets and thirteen datasets derived from seven ST technologies to systematically evaluate the spatial domains identified by eleven state-of-the-art deep learning methods. Our framework highlights the strengths and limitations of each assessment strategy, providing an accessible and reproducible tool for comparative and robust evaluation, and method selection.