{"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/training-free-cryoet-tomogram-segmentation","title":"Training-free CryoET Tomogram Segmentation","arxiv_id":"2407.06833","date":"2024-07-08","proceeding":null,"authors":["Yizhou Zhao","Hengwei Bian","Michael Mu","Mostofa R. Uddin","Zhenyang Li","Xiang Li","Tianyang Wang","Min Xu"],"abstract":"Cryogenic Electron Tomography (CryoET) is a useful imaging technology in structural biology that is hindered by its need for manual annotations, especially in particle picking. Recent works have endeavored to remedy this issue with few-shot learning or contrastive learning techniques. However, supervised training is still inevitable for them. We instead choose to leverage the power of existing 2D foundation models and present a novel, training-free framework, CryoSAM. In addition to prompt-based single-particle instance segmentation, our approach can automatically search for similar features, facilitating full tomogram semantic segmentation with only one prompt. CryoSAM is composed of two major parts: 1) a prompt-based 3D segmentation system that uses prompts to complete single-particle instance segmentation recursively with Cross-Plane Self-Prompting, and 2) a Hierarchical Feature Matching mechanism that efficiently matches relevant features with extracted tomogram features. They collaborate to enable the segmentation of all particles of one category with just one particle-specific prompt. Our experiments show that CryoSAM outperforms existing works by a significant margin and requires even fewer annotations in particle picking. Further visualizations demonstrate its ability when dealing with full tomogram segmentation for various subcellular structures. Our code is available at: https://github.com/xulabs/aitom","url_abs":"https://arxiv.org/abs/2407.06833v1","url_pdf":"https://arxiv.org/pdf/2407.06833v1.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":"training-free-cryoet-tomogram-segmentation","repo_url":"https://github.com/xulabs/aitom","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"GPL-3.0"}}],"tasks":[{"task_slug":"contrastive-learning","task_name":"Contrastive Learning"},{"task_slug":"cryogenic-electron-tomography","task_name":"Cryogenic Electron Tomography"},{"task_slug":"electron-tomography","task_name":"Electron Tomography"},{"task_slug":"few-shot-learning","task_name":"Few-Shot Learning"},{"task_slug":"instance-segmentation","task_name":"Instance Segmentation"},{"task_slug":"segmentation","task_name":"Segmentation"},{"task_slug":"semantic-segmentation","task_name":"Semantic Segmentation"}],"methods":[{"method_slug":"contrastive-learning","method_name":"Contrastive Learning"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}