{"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/accurate-3d-cell-segmentation-using-deep","title":"Accurate 3D Cell Segmentation using Deep Feature and CRF Refinement","arxiv_id":"1902.04729","date":"2019-02-13","proceeding":null,"authors":["Jiaxiang Jiang","Po-Yu Kao","Samuel A. Belteton","Daniel B. Szymanski","B. S. Manjunath"],"abstract":"We consider the problem of accurately identifying cell boundaries and\nlabeling individual cells in confocal microscopy images, specifically, 3D image\nstacks of cells with tagged cell membranes. Precise identification of cell\nboundaries, their shapes, and quantifying inter-cellular space leads to a\nbetter understanding of cell morphogenesis. Towards this, we outline a cell\nsegmentation method that uses a deep neural network architecture to extract a\nconfidence map of cell boundaries, followed by a 3D watershed algorithm and a\nfinal refinement using a conditional random field. In addition to improving the\naccuracy of segmentation compared to other state-of-the-art methods, the\nproposed approach also generalizes well to different datasets without the need\nto retrain the network for each dataset. Detailed experimental results are\nprovided, and the source code is available on GitHub.","url_abs":"http://arxiv.org/abs/1902.04729v1","url_pdf":"http://arxiv.org/pdf/1902.04729v1.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":"accurate-3d-cell-segmentation-using-deep","repo_url":"https://github.com/UCSB-VRL/Purdue3DCell","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"cell-segmentation","task_name":"Cell Segmentation"},{"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}