{"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/3d-mitochondria-instance-segmentation-with","title":"3D Mitochondria Instance Segmentation with Spatio-Temporal Transformers","arxiv_id":"2303.12073","date":"2023-03-21","proceeding":null,"authors":["Omkar Thawakar","Rao Muhammad Anwer","Jorma Laaksonen","Orly Reiner","Mubarak Shah","Fahad Shahbaz Khan"],"abstract":"Accurate 3D mitochondria instance segmentation in electron microscopy (EM) is a challenging problem and serves as a prerequisite to empirically analyze their distributions and morphology. Most existing approaches employ 3D convolutions to obtain representative features. However, these convolution-based approaches struggle to effectively capture long-range dependencies in the volume mitochondria data, due to their limited local receptive field. To address this, we propose a hybrid encoder-decoder framework based on a split spatio-temporal attention module that efficiently computes spatial and temporal self-attentions in parallel, which are later fused through a deformable convolution. Further, we introduce a semantic foreground-background adversarial loss during training that aids in delineating the region of mitochondria instances from the background clutter. Our extensive experiments on three benchmarks, Lucchi, MitoEM-R and MitoEM-H, reveal the benefits of the proposed contributions achieving state-of-the-art results on all three datasets. Our code and models are available at https://github.com/OmkarThawakar/STT-UNET.","url_abs":"https://arxiv.org/abs/2303.12073v1","url_pdf":"https://arxiv.org/pdf/2303.12073v1.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":"3d-mitochondria-instance-segmentation-with","repo_url":"https://github.com/omkarthawakar/stt-unet","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"decoder","task_name":"Decoder"},{"task_slug":"instance-segmentation","task_name":"Instance Segmentation"},{"task_slug":"semantic-segmentation","task_name":"Semantic 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}