{"ID":2871224,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_url":"https://arxiv.org/abs/2509.11063","arxiv_id":"2509.11063","title":"Organoid Tracker: A SAM2-Powered Platform for Zero-shot Cyst Analysis in Human Kidney Organoid Videos","abstract":"Recent advances in organoid models have revolutionized the study of human kidney disease mechanisms and drug discovery by enabling scalable, cost-effective research without the need for animal sacrifice. Here, we present a kidney organoid platform optimized for efficient screening in polycystic kidney disease (PKD). While these systems generate rich spatial-temporal microscopy video datasets, current manual approaches to analysis remain limited to coarse classifications (e.g., hit vs. non-hit), often missing valuable pixel-level and longitudinal information. To help overcome this bottleneck, we developed Organoid Tracker, a graphical user interface (GUI) platform designed with a modular plugin architecture, which empowers researchers to extract detailed, quantitative metrics without programming expertise. Built on the cutting-edge vision foundation model Segment Anything Model 2 (SAM2), Organoid Tracker enables zero-shot segmentation and automated analysis of spatial-temporal microscopy videos. It quantifies key metrics such as cyst formation rate, growth velocity, and morphological changes, while generating comprehensive reports. By providing an extensible, open-source framework, Organoid Tracker offers a powerful solution for improving and accelerating research in kidney development, PKD modeling, and therapeutic discovery. The platform is publicly available as open-source software at https://github.com/hrlblab/OrganoidTracker.","short_abstract":"Recent advances in organoid models have revolutionized the study of human kidney disease mechanisms and drug discovery by enabling scalable, cost-effective research without the need for animal sacrifice. Here, we present a kidney organoid platform optimized for efficient screening in polycystic kidney disease (PKD). Wh...","url_abs":"https://arxiv.org/abs/2509.11063","url_pdf":"https://arxiv.org/pdf/2509.11063v1","authors":"[\"Xiaoyu Huang\",\"Lauren M Maxson\",\"Trang Nguyen\",\"Cheng Jack Song\",\"Yuankai Huo\"]","published":"2025-09-14T03:11:01Z","proceeding":"cs.CV","tasks":"[\"cs.CV\"]","methods":"[\"Generative Adversarial Network\"]","has_code":false,"code_links":[{"ID":609837,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_id":2871224,"paper_url":"https://arxiv.org/abs/2509.11063","paper_title":"Organoid Tracker: A SAM2-Powered Platform for Zero-shot Cyst Analysis in Human Kidney Organoid Videos","repo_url":"https://github.com/hrlblab/OrganoidTracker","is_official":false,"mentioned_in_paper":false,"mentioned_in_github":true,"github_stars":0}]}