Stitching, Fine-tuning, Re-training: A SAM-enabled Framework for Semi-supervised 3D Medical Image Segmentation

TL;DR

This paper introduces a three-stage semi-supervised framework called SFR, leveraging SAM for efficient 3D medical image segmentation with limited annotations, significantly improving performance over existing methods.

Contribution

The paper proposes a novel SFR framework that combines stitching, fine-tuning, and re-training, enhancing semi-supervised 3D medical segmentation with minimal annotations.

Findings

SFR improves Dice score from 29.68% to 74.40% on LA dataset.

SFR achieves significant performance gains across five datasets.

SFR$^+$ further enhances results with confidence-based selective training.

Abstract

Segment Anything Model (SAM) fine-tuning has shown remarkable performance in medical image segmentation in a fully supervised manner, but requires precise annotations. To reduce the annotation cost and maintain satisfactory performance, in this work, we leverage the capabilities of SAM for establishing semi-supervised medical image segmentation models. Rethinking the requirements of effectiveness, efficiency, and compatibility, we propose a three-stage framework, i.e., Stitching, Fine-tuning, and Re-training (SFR). The current fine-tuning approaches mostly involve 2D slice-wise fine-tuning that disregards the contextual information between adjacent slices. Our stitching strategy mitigates the mismatch between natural and 3D medical images. The stitched images are then used for fine-tuning SAM, providing robust initialization of pseudo-labels. Afterwards, we train a 3D semi-supervised segmentation model while maintaining the same parameter size as the conventional segmenter such as V-Net. Our SFR framework is plug-and-play, and easily compatible with various popular semi-supervised methods. We also develop an extended framework SFR$^+$ with selective fine-tuning and re-training through confidence estimation. Extensive experiments validate that our SFR and SFR$^+$ achieve significant improvements in both moderate annotation and scarce annotation across five datasets. In particular, SFR framework improves the Dice score of Mean Teacher from 29.68% to 74.40% with only one labeled data of LA dataset.