{"ID":2845530,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_url":"https://arxiv.org/abs/2511.04811","arxiv_id":"2511.04811","title":"An Active Learning Pipeline for Biomedical Image Instance Segmentation with Minimal Human Intervention","abstract":"Biomedical image segmentation is critical for precise structure delineation and downstream analysis. Traditional methods often struggle with noisy data, while deep learning models such as U-Net have set new benchmarks in segmentation performance. nnU-Net further automates model configuration, making it adaptable across datasets without extensive tuning. However, it requires a substantial amount of annotated data for cross-validation, posing a challenge when only raw images but no labels are available. Large foundation models offer zero-shot generalizability, but may underperform on specific datasets with unique characteristics, limiting their direct use for analysis. This work addresses these bottlenecks by proposing a data-centric AI workflow that leverages active learning and pseudo-labeling to combine the strengths of traditional neural networks and large foundation models while minimizing human intervention. The pipeline starts by generating pseudo-labels from a foundation model, which are then used for nnU-Net's self-configuration. Subsequently, a representative core-set is selected for minimal manual annotation, enabling effective fine-tuning of the nnU-Net model. This approach significantly reduces the need for manual annotations while maintaining competitive performance, providing an accessible solution for biomedical researchers to apply state-of-the-art AI techniques in their segmentation tasks. The code is available at https://github.com/MMV-Lab/AL_BioMed_img_seg.","short_abstract":"Biomedical image segmentation is critical for precise structure delineation and downstream analysis. Traditional methods often struggle with noisy data, while deep learning models such as U-Net have set new benchmarks in segmentation performance. nnU-Net further automates model configuration, making it adaptable across...","url_abs":"https://arxiv.org/abs/2511.04811","url_pdf":"https://arxiv.org/pdf/2511.04811v1","authors":"[\"Shuo Zhao\",\"Yu Zhou\",\"Jianxu Chen\"]","published":"2025-11-06T21:07:26Z","proceeding":"cs.CV","tasks":"[\"cs.CV\",\"cs.AI\",\"cs.LG\"]","methods":"[]","has_code":false,"code_links":[{"ID":607369,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_id":2845530,"paper_url":"https://arxiv.org/abs/2511.04811","paper_title":"An Active Learning Pipeline for Biomedical Image Instance Segmentation with Minimal Human Intervention","repo_url":"https://github.com/MMV-Lab/AL_BioMed_img_seg","is_official":false,"mentioned_in_paper":false,"mentioned_in_github":true,"github_stars":0}]}