Segment Anything in Medical Images with nnUNet

Raphael Stock, Yannick Kirchhoff, Maximilian Rouven Rokuss, Ashis Ravindran, Klaus Maier-Hein

Keywords: Medical Image Segmentation, nnUNet, Bounding Box Prompts, CPU Inference

Abstract: In this paper, we present an enhanced medical image segmentation approach leveraging the nnUNet framework, specifically tailored to integrate bounding box prompts for improved segmentation accuracy in resource-constrained environments. By incorporating these prompts as binary masks in an additional input channel, we enable more precise and context-aware segmentation. Our methodology employs a 2D slice-wise approach optimized for CPU-based inference through just-in-time (JIT) compiled functions, ensuring efficient processing on standard clinical equipment. Our solution demonstrates robust performance, achieving an average Dice Similarity Coefficient (DSC) of 80.98\% and a Normalized Surface Dice (NSD) of 83.23\% across multiple modalities in the validation set. This indicates its practical applicability and effectiveness in real-world clinical settings, where computational resources may be limited. By focusing on both accuracy and efficiency, our approach makes advanced segmentation technology accessible to a broader range of healthcare providers, facilitating enhanced clinical decision-making and patient care.

Submission Number: 11