{"id":78983,"date":"2026-04-09T10:42:42","date_gmt":"2026-04-09T08:42:42","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=78983"},"modified":"2026-04-16T16:33:58","modified_gmt":"2026-04-16T14:33:58","slug":"spatial-transcriptomics-portal-seeing-gene-expression-in-a-spatial-context","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science-technology\/spatial-transcriptomics-portal-seeing-gene-expression-in-a-spatial-context\/","title":{"rendered":"Spatial Transcriptomics Portal: Seeing gene expression in a spatial context"},"content":{"rendered":"\n<p>EMBL-EBI\u2019s BioImage Archive and Functional Genomics teams have joined forces to develop the <a href=\"https:\/\/www.ebi.ac.uk\/spatial-transcriptomics\/\">Spatial Transcriptomics Portal<\/a>. This is a pilot resource that combines imaging and molecular data to show which genes are active in which cells, and precisely where those cells are located within tissues.&nbsp;&nbsp;<\/p>\n\n\n\n<p>Until now, there has been no unified platform linking spatial information with molecular gene expression. This new resource aims to provide scientists with a single entry point for community updates, data access guidance, and existing research in spatial transcriptomics.<\/p>\n\n\n\n<article class=\"vf-card vf-card--brand vf-card--bordered vf-u-margin__bottom--800\" default>\n  <div class=\"vf-card__content | vf-stack vf-stack--400\">\n      <h3 class=\"vf-card__heading\">\n      What is spatial transcriptomics?    <\/h3>\n                <p class=\"vf-card__text\"><\/p><p><span style=\"font-weight: 400;\">Spatial transcriptomics is a molecular profiling technique that allows scientists to map gene activity across tissues. When a gene is active, a cell produces a molecule called RNA. Standard transcriptomics tells us which RNA molecules are present, but not where this activity occurs within the tissue. <\/span><\/p>\r\n\r\n<p><span style=\"font-weight: 400;\"> Spatial transcriptomics is like having a map of a city. Previous methods could tell you the city had two hospitals and a supermarket, but not where they were. Now, we can see exactly where these \u2018buildings\u2019 are located. This allows us to understand the context. For example, if a hospital is next to a ski slope, the reason for a high rate of injuries in its emergency department becomes clear. In biology, knowing where a gene is expressed tells us how cells interact, and how diseases like cancer progress at a cellular level.\u00a0<\/span><\/p>\n      <\/div>\n<\/article>\n\n\n\n\n<h2 class=\"wp-block-heading\"><strong>The Spatial Transcriptomics Portal<\/strong><\/h2>\n\n\n\n<p>Spatial transcriptomics sits at the intersection of sequencing and imaging. The new portal acts as a unified bridge between these two domains, providing a single entry point for researchers to navigate EMBL-EBI\u2019s diverse spatial data resources.&nbsp;<\/p>\n\n\n\n<p>The core technical achievement of this pilot phase is the introduction of harmonised metadata standards developed jointly by the <a href=\"https:\/\/www.ebi.ac.uk\/about\/teams\/functional-genomics\/\">Functional Genomics<\/a> and <a href=\"https:\/\/www.ebi.ac.uk\/about\/teams\/bioimage-archive\/\">BioImage Archive<\/a> teams. By defining a common framework for both imaging and sequencing technologies, these standards provide the foundation for a resource that will eventually allow diverse datasets to be retrieved and compared as a single, cohesive entity.&nbsp;<\/p>\n\n\n\n<p>\u201cThis is a direct response to the community\u2019s needs, and we welcome feedback on these standards as we work to improve integrated data management at scale,\u201d said <a href=\"https:\/\/www.ebi.ac.uk\/people\/person\/christina-ernst\/\">Christina Ernst, Functional Genomics Team Leader<\/a> at EMBL-EBI.<\/p>\n\n\n\n<p>Currently in Phase 1, the portal serves as a strategic signpost for the community. It provides immediate guidance on existing data solutions while establishing a transparent roadmap for the future of integrated spatial data at EMBL-EBI.&nbsp;<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"619\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2026\/03\/phases1-1024x619.png\" alt=\"\" class=\"wp-image-78989\" srcset=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2026\/03\/phases1-1024x619.png 1024w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2026\/03\/phases1-300x181.png 300w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2026\/03\/phases1-768x464.png 768w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2026\/03\/phases1.png 1198w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>This approach ensures reliability and versatility while preparing the resource for broader community use.&nbsp;<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Looking ahead<\/strong><\/h2>\n\n\n\n<p>The integration of imaging and spatial gene expression data also creates opportunities for AI-driven analysis. \u201cSpatial transcriptomics is rapidly growing in popularity in life sciences. There is a huge potential, both for enabling new biological discoveries, and for training the next generation of AI models,\u201d said <a href=\"https:\/\/www.ebi.ac.uk\/people\/person\/matthew-hartley\/\">Matthew Hartley, BioImage Archive Team Leader<\/a> at EMBL-EBI.&nbsp;<\/p>\n\n\n\n<p>The Spatial Transcriptomics Portal represents a key step toward integrating cross-modality data in life sciences. By providing a unified, accessible resource, EMBL-EBI supports scientists to explore spatial gene expression and gain new insights into biology and disease.<\/p>\n\n\n\n\n","protected":false},"excerpt":{"rendered":"<p>New portal integrates imaging and gene expression data to map gene activity across tissues.<\/p>\n","protected":false},"author":187,"featured_media":79055,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[17591,11058],"tags":[858,36,1960,13930,13932],"embl_taxonomy":[11092,18859,2906,11976,19035],"class_list":["post-78983","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science-technology","category-updates-from-data-resources","tag-bioimage-archive","tag-embl-ebi","tag-functional-genomics","tag-spatial-omics","tag-transcriptomics","embl_taxonomy-bioimage-archive","embl_taxonomy-christina-ernst","embl_taxonomy-embl-ebi","embl_taxonomy-functional-genomics","embl_taxonomy-matthew-hartley"],"acf":{"vfwp-news_embl_taxonomy":[2906,11092,11976,18859,19035],"featured":true,"show_featured_image":false,"field_target_display":"both","field_article_language":{"value":"english","label":"English"},"article_intro":"<p>New portal integrates imaging and gene expression data to map gene activity across tissues<\/p>\n","related_links":[{"link_description":"A universal framework for spatial biology","link_url":"https:\/\/www.embl.org\/news\/science-technology\/a-universal-framework-for-spatial-biology\/"},{"link_description":"Light-Seq: from images to sequences in context","link_url":"https:\/\/www.embl.org\/news\/science\/light-seq-from-images-to-sequences-in-context\/"},{"link_description":"Imaging-based spatial-omics: EMBO Practical Course at EMBL Rome ","link_url":"https:\/\/www.embl.org\/news\/lab-matters\/imaging-based-spatial-omics-embo-practical-course-at-embl-rome\/"}],"source_article":false,"in_this_article":false,"press_contact":"None","article_translations":false,"languages":"","vf_locked":false},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"18699e63-ed43-40c6-8d1c-203db7ed72ee\";i:2;s:36:\"11b1073a-99ae-48c9-8494-99f302f7579d\";}","parents":[],"name":["BioImage Archive"],"slug":"bioimage-archive","description":"What &gt; 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