提出自适应降噪注意力机制,提升显微图像中微管分割精度
A novel attention mechanism for noise-adaptive and robust segmentation of microtubules in microscopy images
- 设计噪声自适应注意力模块,动态调节不同噪声水平下的特征权重
- 在合成与真实数据上均优于对比模型,参数量少且性能强
- 可迁移至血管、神经等细长结构分割,适合资源受限场景
微管等细胞骨架丝状结构的分割对研究细胞过程至关重要,但因其细密交错、成像受限,分割难度大。深度学习在复杂条件下性能下降,且存在标注困难与类别不平衡问题。本文提出一种新型噪声自适应注意力机制,扩展Squeeze-and-Excitation模块以动态响应不同噪声水平,并集成至带残差编码器的U-Net解码器中,构建轻量高效模型ASE_Res_UNet。同时设计合成数据生成策略,确保细丝结构在噪声图像中的精确标注。通过系统评估损失函数与评价指标,有效缓解类别不平衡问题。ASE_Res_UNet在合成数据上显著优于消融模型;在新标注的真实显微图像数据集和重新标注的数据集上,表现媲美依赖预训练模型的先进方法。该模型还展现出对血管、神经等其他曲线索结构的强迁移能力,适用于多样成像条件。
原文摘要 · Abstract (English)
Segmenting cytoskeletal filaments in microscopy images is essential for studying their roles in cellular processes. However, this task is highly challenging due to the fine, densely packed, and intertwined nature of these structures. Imaging limitations further complicate analysis. While deep learning has advanced segmentation of large, well-defined biological structures, its performance often degrades under such adverse conditions. Additional challenges include obtaining precise annotations for curvilinear structures and managing severe class imbalance during training. We introduce a novel noise-adaptive attention mechanism that extends the Squeeze-and-Excitation (SE) module to dynamically adjust to varying noise levels. Integrated into a U-Net decoder with residual encoder blocks, this yields ASE_Res_UNet, a lightweight yet high-performance model. We also developed a synthetic dataset generation strategy that ensures accurate annotations of fine filaments in noisy images. We systematically evaluated loss functions and metrics to mitigate class imbalance, ensuring robust performance assessment. ASE_Res_UNet effectively segmented microtubules in noisy synthetic images, outperforming its ablated variants. It also demonstrated superior segmentation compared to models with alternative attention mechanisms or distinct architectures, while requiring fewer parameters, making it efficient for resource-constrained environments. Evaluation on a newly curated real microscopy dataset and a recently reannotated dataset highlighted ASE_Res_UNet's effectiveness in segmenting microtubules beyond synthetic images. For these datasets, ASE_Res_UNet was competitive with a recent synthetic data-driven approach that shares two cytoskeleton pretrained models. Importantly, ASE_Res_UNet showed strong transferability to other curvilinear structures (blood vessels and nerves) across diverse imaging conditions.
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