{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/large-scale-multi-hypotheses-cell-tracking","title":"Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps","arxiv_id":"2308.04526","date":"2023-08-08","proceeding":null,"authors":["Jordão Bragantini","Merlin Lange","Loïc Royer"],"abstract":"In this work, we describe a method for large-scale 3D cell-tracking through a segmentation selection approach. The proposed method is effective at tracking cells across large microscopy datasets on two fronts: (i) It can solve problems containing millions of segmentation instances in terabyte-scale 3D+t datasets; (ii) It achieves competitive results with or without deep learning, which requires 3D annotated data, that is scarce in the fluorescence microscopy field. The proposed method computes cell tracks and segments using a hierarchy of segmentation hypotheses and selects disjoint segments by maximizing the overlap between adjacent frames. We show that this method achieves state-of-the-art results in 3D images from the cell tracking challenge and has a faster integer linear programming formulation. Moreover, our framework is flexible and supports segmentations from off-the-shelf cell segmentation models and can combine them into an ensemble that improves tracking. The code is available https://github.com/royerlab/ultrack.","url_abs":"https://arxiv.org/abs/2308.04526v2","url_pdf":"https://arxiv.org/pdf/2308.04526v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"large-scale-multi-hypotheses-cell-tracking","repo_url":"https://github.com/royerlab/ultrack","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"cell-segmentation","task_name":"Cell Segmentation"},{"task_slug":"cell-tracking","task_name":"Cell Tracking"},{"task_slug":"segmentation","task_name":"Segmentation"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}