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However, within these frameworks, spatial information is often reduced to locations and relationships between molecular profiles, without fully leveraging the wealth of sub-micron morphological detail and histological knowledge available. Advances in computer vision-based artificial intelligence (AI) are opening exciting new avenues beyond conventional bioinformatics approaches by modeling complex histological patterns and linking morphology to molecular states. More excitingly, they bring fresh perspectives to potentially address key limitations of ST, including its high cost, limited clinical applicability, and reliance on 2D analysis of inherently 3D tissues. For instance, models that predict ST directly from histology images enable virtual sequencing, drastically reducing costs while integrating morphological insights from pathology with molecular biomarkers, thus accelerating clinical translation. Moreover, computer vision techniques can reconstruct pixel-aligned 3D tissue models, overcoming the technical barriers of 2D acquisition and advancing 3D spatial omics analytics. In this paper, we present the first systematic survey of computer vision AI models for ST analytics, categorizing approaches across architectures, learning paradigms, tasks, and datasets, and tracing their technological evolution. We highlight key challenges and future directions, offering a panoramic perspective on vision-driven ST and its potential to transform both basic research and clinical practice. The curated collection of vision-driven ST papers is available at https:\/\/github.com\/hrlblab\/computer_vision_spatial_omics.<\/jats:p>","DOI":"10.1093\/bib\/bbag255","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T11:27:22Z","timestamp":1777980442000},"source":"Crossref","is-referenced-by-count":0,"title":["A comprehensive survey of computer vision methods for spatial transcriptomics"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6610-9808","authenticated-orcid":false,"given":"Junchao","family":"Zhu","sequence":"first","affiliation":[{"name":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruining","family":"Deng","sequence":"additional","affiliation":[{"name":"Weill Cornell Medicine , 1300 York Ave, New York, NY 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Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juming","family":"Xiong","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering , Vanderbilt University, 2301 Vanderbilt Place, Nashville, TN 37235,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanfan","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengyi","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuechen","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marilyn","family":"Lionts","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vanderbilt University , 2301 Vanderbilt Place, Nashville, TN 37235,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yucheng","family":"Tang","sequence":"additional","affiliation":[{"name":"NVIDIA, 2788 San Tomas Expressway , Santa Clara, CA 95051,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daguang","family":"Xu","sequence":"additional","affiliation":[{"name":"NVIDIA, 2788 San Tomas Expressway , Santa Clara, CA 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