{"id":2746,"date":"2025-05-14T08:54:43","date_gmt":"2025-05-14T00:54:43","guid":{"rendered":"https:\/\/medicine.nus.edu.sg\/trp\/immunology\/?post_type=research-highlights&#038;p=2746"},"modified":"2025-05-15T08:58:58","modified_gmt":"2025-05-15T00:58:58","slug":"digitalized-organoids-integrated-pipelinefor-high-speed-3d-analysis-of-organoidstructures-using-multilevel-segmentationand-cellular-topology","status":"publish","type":"research-highlights","link":"https:\/\/medicine.nus.edu.sg\/trp\/immunology\/news-events\/research-highlights\/digitalized-organoids-integrated-pipelinefor-high-speed-3d-analysis-of-organoidstructures-using-multilevel-segmentationand-cellular-topology\/","title":{"rendered":"Digitalized organoids: integrated pipelinefor high-speed 3D analysis of organoidstructures using multilevel segmentationand cellular topology"},"content":{"rendered":"<p><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">Organoids replicate tissue architecture and function and offer a unique <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">opportunity to explore the impact of external perturbations in vitro. <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">However, conducting large-scale screening procedures to investigate <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">the effects of various stresses on cellular morphology and topology <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">in these systems poses important challenges, including limitations in <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">high-resolution three-dimensional (3D) imaging and accessible 3D analysis <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">platforms. In this study, we introduce an AI-based multilevel segmentation <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">and cellular topology pipeline for screening morphology and topology <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">modifications in 3D cell culture at both the nuclear and cytoplasmic levels, <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">as well as at the whole-organoid scale. We demonstrate the versatility of <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">our approach through proof-of-concept experiments, encompassing <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">well-characterized conditions and poorly explored mechanical stressors <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">such as microgravity. By offering a user-friendly interface named <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">3DCellScope and a comprehensive set of tools for discovery-like assays in <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">screening 3D organoid models, our pipeline demonstrates wide-ranging <\/span><span class=\"current-selection\" dir=\"ltr\" role=\"presentation\">potential for applications in biomedical research.<\/span><\/p>\n<p><a href=\"https:\/\/www.nature.com\/articles\/s41592-025-02685-4.epdf?sharing_token=jDqiyZ5okjxNhnwP35sl6NRgN0jAjWel9jnR3ZoTv0M5CAI3ft2QQ4KrVksDyd3NNIWJ3Gbc7AqxbUhOZoH5HzjeECI9Hm3TVf-fnZ8b7n_sdtpSoqQB770htZqRh5ojqBuAKq2isS4rfDpjB2Yuuz5Bqup-_YoOBwmBEOPB3zg%3D\">Click here for the details of the publication.<\/a><\/p>\n<p>&nbsp;<\/p>\n","protected":false},"featured_media":2747,"template":"","research-hightlights-category":[38],"class_list":["post-2746","research-highlights","type-research-highlights","status-publish","has-post-thumbnail","hentry","research-hightlights-category-publications"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.0 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Digitalized organoids: integrated pipelinefor high-speed 3D analysis of organoidstructures using multilevel segmentationand cellular topology - Immunology<\/title>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Digitalized organoids: integrated pipelinefor high-speed 3D analysis of organoidstructures using multilevel segmentationand cellular topology - Immunology\" \/>\n<meta property=\"og:description\" content=\"Organoids replicate tissue architecture and function and offer a unique opportunity to explore the impact of external perturbations in vitro. However, conducting large-scale screening procedures to investigate the effects of various stresses on cellular morphology and topology in these systems poses important challenges, including limitations in high-resolution three-dimensional (3D) imaging and accessible 3D analysis platforms. 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