{"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/diffkillr-killing-and-recreating","title":"DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images","arxiv_id":"2410.03058","date":"2024-10-04","proceeding":null,"authors":["Chen Liu","Danqi Liao","Alejandro Parada-Mayorga","Alejandro Ribeiro","Marcello DiStasio","Smita Krishnaswamy"],"abstract":"The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for biomedical research and clinical diagnostics. However, accurately annotating densely packed information in these images remains a major challenge. To address this, we introduce DiffKillR, a novel framework that reframes cell annotation as the combination of archetype matching and image registration tasks. DiffKillR employs two complementary neural networks: one that learns a diffeomorphism-invariant feature space for robust cell matching and another that computes the precise warping field between cells for annotation mapping. Using a small set of annotated archetypes, DiffKillR efficiently propagates annotations across large microscopy images, reducing the need for extensive manual labeling. More importantly, it is suitable for any type of pixel-level annotation. We will discuss the theoretical properties of DiffKillR and validate it on three microscopy tasks, demonstrating its advantages over existing supervised, semi-supervised, and unsupervised methods.","url_abs":"https://arxiv.org/abs/2410.03058v1","url_pdf":"https://arxiv.org/pdf/2410.03058v1.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":"diffkillr-killing-and-recreating","repo_url":"https://github.com/KrishnaswamyLab/DiffKillR","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"electron-microscopy-image-segmentation","task_name":"Electron Microscopy Image Segmentation"},{"task_slug":"image-registration","task_name":"Image Registration"},{"task_slug":"image-segmentation","task_name":"Image Segmentation"},{"task_slug":"medical-image-segmentation","task_name":"Medical Image Segmentation"},{"task_slug":"self-supervised-learning","task_name":"Self-Supervised Learning"},{"task_slug":"unsupervised-image-segmentation","task_name":"Unsupervised Image Segmentation"},{"task_slug":"whole-slide-images","task_name":"whole slide images"}],"methods":[{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2410.03058","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2410.03058"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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