Advances in plant spatial multi-omics data analysis

Recent advances in plant spatial omics, including transcriptomics and metabolomics, have enabled fine-scale cellular insights by registering spatial information. Combining spatial approaches with droplet-based single-cell technologies has further enhanced our understanding of many complex biological processes. However, the unique features of plants, such as rigid cell walls and size variability, require adaptation of mammalian-derived analytical methods. This review summarizes current strategies for acquiring plant spatial multi-omics data, with a focus on widely accessible commercial platforms. We also outline analysis workflows, from preprocessing to downstream interpretation, and provide a practical tutorial using demonstration datasets. This resource offers researchers a concise guide to experimental and computational approaches for plant spatial multi-omics.