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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.<\/jats:p>","DOI":"10.1093\/plcell\/koag282","type":"journal-article","created":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T11:42:45Z","timestamp":1789213365000},"source":"Crossref","is-referenced-by-count":0,"title":["Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8654-0977","authenticated-orcid":false,"given":"Min-Yao","family":"Jhu","sequence":"first","affiliation":[{"name":"Crop Science Centre, Department of Plant Sciences, University of Cambridge , Cambridge CB3 0LE ,","place":["United Kingdom"]},{"name":"Donald Danforth Plant Science Center , St. Louis, MO 63132 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3089-2284","authenticated-orcid":false,"given":"Max","family":"Minne","sequence":"additional","affiliation":[{"name":"RIKEN Center for Sustainable Resource Science , Tsurumi, Yokohama, Kanagawa 230-0045 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8720-0133","authenticated-orcid":false,"given":"Ziliang","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of Georgia , Athens, GA 30602 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0476-9699","authenticated-orcid":false,"given":"Hannah","family":"D\u00f6rpholz","sequence":"additional","affiliation":[{"name":"Institute of Bio- and Geosciences (IBG-4: Bioinformatics), CEPLAS, BioSC, Forschungszentrum J\u00fclich , J\u00fclich 52428 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7898-1799","authenticated-orcid":false,"given":"Jie","family":"Yao","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of Georgia , Athens, GA 30602 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1104-6931","authenticated-orcid":false,"given":"M Shahid","family":"Mukhtar","sequence":"additional","affiliation":[{"name":"Department of Genetics and Biochemistry, Clemson University. Clemson , SC 29634 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4615-7452","authenticated-orcid":false,"given":"Fern","family":"Mathieu","sequence":"additional","affiliation":[{"name":"University of California Davis Genome Center, University of California. Davis , CA 95616 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0004-0654","authenticated-orcid":false,"given":"Marta","family":"Peirats-Llobet","sequence":"additional","affiliation":[{"name":"Department of Ecological, Plant and Animal Sciences, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University , Bundoora, Victoria 3086 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8352-8956","authenticated-orcid":false,"given":"Travis","family":"Lee","sequence":"additional","affiliation":[{"name":"Plant Biology Laboratory, The Salk Institute for Biological Studies , La Jolla, CA 92037 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3005-597X","authenticated-orcid":false,"given":"Pau","family":"Formosa-Jordan","sequence":"additional","affiliation":[{"name":"Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, CEPLAS , Cologne 50829 ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9160-3111","authenticated-orcid":false,"given":"Siyu","family":"Song","sequence":"additional","affiliation":[{"name":"The Sainsbury Laboratory, University of East Anglia , Norwich Research Park, Norwich NR4 7UH ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7419-9129","authenticated-orcid":false,"given":"Marc","family":"Libault","sequence":"additional","affiliation":[{"name":"Division of Plant Science and Technology, Interdisciplinary Plant Group, Christopher S. 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