用轻量级模型自动识别病理切片中的模糊、褶皱等问题,提升图像质量控制效率。
Semantic Segmentation Based Quality Control of Histopathology Whole Slide Images
- 采用多个轻量级深度学习模型实现多类区域分割,兼顾精度与速度。
- 在超过1.1万张来自28个器官的TCGA数据上验证,效果优于传统方法。
- 可直接用于科研或临床前处理,降低人工标注成本,支持快速部署。
我们开发了一套用于病理全切片图像(WSI)质量控制(QC)的软件流程,能够对不同等级的模糊、组织区域、组织褶皱和笔迹等进行分割。鉴于处理WSI时GPU的必要性和普及性,该流程采用多个轻量级深度学习模型,在准确性和速度之间取得平衡。该流程在TCGA数据集上进行了全面评估,该数据集是目前最大的公开WSI数据集,包含超过11,000张来自28个器官的组织病理图像。与非深度学习的先前工作相比,本方法在所有器官上均实现了稳定的分割性能提升。为减少组织和模糊区域的标注负担,通过HistoROI分类工具识别标签后,自动拼接各WSI的图像块(子图)生成标注数据。由于训练的QC流程具有通用性且经过广泛测试,其潜在影响广泛,可用于任何WSI队列的自动化预处理,从而提升大规模病理图像分析在研究与临床中的准确性与可靠性。我们已将训练好的模型、训练脚本、训练数据及推理结果公开于https://github.com/abhijeetptl5/wsisegqc,供研究社区即开即用或进一步适配新数据集与应用。
原文摘要 · Abstract (English)
We developed a software pipeline for quality control (QC) of histopathology whole slide images (WSIs) that segments various regions, such as blurs of different levels, tissue regions, tissue folds, and pen marks. Given the necessity and increasing availability of GPUs for processing WSIs, the proposed pipeline comprises multiple lightweight deep learning models to strike a balance between accuracy and speed. The pipeline was evaluated in all TCGAs, which is the largest publicly available WSI dataset containing more than 11,000 histopathological images from 28 organs. It was compared to a previous work, which was not based on deep learning, and it showed consistent improvement in segmentation results across organs. To minimize annotation effort for tissue and blur segmentation, annotated images were automatically prepared by mosaicking patches (sub-images) from various WSIs whose labels were identified using a patch classification tool HistoROI. Due to the generality of our trained QC pipeline and its extensive testing the potential impact of this work is broad. It can be used for automated pre-processing any WSI cohort to enhance the accuracy and reliability of large-scale histopathology image analysis for both research and clinical use. We have made the trained models, training scripts, training data, and inference results publicly available at https://github.com/abhijeetptl5/wsisegqc, which should enable the research community to use the pipeline right out of the box or further customize it to new datasets and applications in the future.
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