Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward

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Abstract
Spatial omics technologies provide new opportunities for plant biology by enabling molecular profiling within structurally intact tissues, revealing spatially organized cell states, developmental gradients, and regulatory interactions. While spatial transcriptomics has driven early advances, the field is rapidly expanding toward integrated spatial multi-omics by combining single-cell and spatial transcriptomic, epigenomic, proteomic, and metabolomic data. These approaches offer new opportunities to study development, physiology, and plant biotic and abiotic interactions in spatially preserved cellular contexts. However, despite rapid adoption, the field remains constrained by plant-specific challenges when applying technologies largely developed for animal systems. Compared with animal systems, plant tissues pose additional challenges due to rigid cell walls and diverse chemistries, complicating sample preparation, cell and subcellular segmentation, signal detection, and data integration. As a result, many studies rely on bespoke protocols and analysis pipelines that are often difficult to reproduce or generalize. Here, we provide a practical, solution-oriented synthesis of current bottlenecks across experimental and computational pipelines, highlight emerging strategies to overcome these limitations, and propose a roadmap for community-driven protocol sharing, benchmarking, and integration across spatial and multi-omics modalities. Addressing these challenges will be essential to establish spatial omics as a routine and scalable tool for plant biology.
Funding Information
  • Japan Science and Technology Agency (ASPIRE JPMJAP2306)
  • National Science Foundation (NSF OISE-2020459)
  • Cluster of Excellence on Plant Sciences (EXC2048)
  • Max-Planck-Gesellschaft
  • Gatsby Charitable Foundation
  • Biotechnology and Biological Sciences Research Council (BB/Y002997/1)
  • U.S. Department of Energy
  • Biological and Environmental Research (DE-SC0023338)
  • Biological and Environmental Research (DE-SC0025995)
  • U.S. DOE-BER Bioimaging Program (DE-SC0018459)
  • Shurl and Kay Curci Foundation
  • Donna and Benjamin M. Rosen Bioengineering Center, California Institute of Technology
  • Resnick Sustainability Institute for Science, Energy and Sustainability, California Institute of Technology (MCB-2544734)
  • Deutsche Forschungsgemeinschaft (44207744)
  • Helmholtz Association (ZT-I-PF-3-091)
  • Neurosciences Foundation (IOS-2038872)
  • Neurosciences Foundation (OIA-2418230)
  • ARC Centre of Excellence Plants for Space (PID2022-140719NB-I00)
  • ARC Centre of Excellence Plants for Space (MICIU/AEI/10.13039/501100011033)
  • ARC Centre of Excellence Plants for Space (CEX2020-000999-S)
  • ARC Centre of Excellence Plants for Space (MICIU/AEI/10.13039/501100011033)
  • Japan Society for the Promotion of Science (P25086)

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