The automatic registration of differently stained whole slide images (WSIs) is crucial for improving diagnosis and prognosis by fusing complementary information emerging from different visible structures. It is also useful to quickly transfer annotations between consecutive or restained slides, thus significantly reducing the annotation time and associated costs. Nevertheless, the slide preparation is different for each stain and the tissue undergoes complex and large deformations. Therefore, a robust, efficient, and accurate registration method is highly desired by the scientific community and hospitals specializing in digital pathology. We propose a two-step hybrid method consisting of (i) deep learning- and feature-based initial alignment algorithm, and (ii) intensity-based nonrigid registration using the instance optimization. The proposed method does not require any fine-tuning to a particular dataset and can be used directly for any desired tissue type and stain. The method scored 1st place in the ACROBAT 2023 challenge. We evaluated using three open datasets: (i) ANHIR, (ii) ACROBAT, and (iii) HyReCo, and performed several ablation studies concerning the resolution used for registration and the initial alignment robustness and stability. The method achieves the most accurate results for the ACROBAT dataset, the cell-level registration accuracy for the restained slides from the HyReCo dataset, and is among the best methods evaluated on the ANHIR dataset. The method does not require any fine-tuning to a new datasets and can be used out-of-the-box for other types of microscopic images. The method is incorporated into the DeeperHistReg framework, allowing others to directly use it to register, transform, and save the WSIs at any desired pyramid level. The proposed method is a significant contribution to the WSI registration, thus advancing the field of digital pathology.

我们提出了一个两步骤混合方法，包括深度学习和特征提取的初始对齐算法以及基于强度的非刚性配准。该方法不需要对特定数据集进行微调，可直接用于任何所需的组织类型和染色剂。该方法在ACROBAT数据集上获得了最准确的结果，在HyReCo数据集上实现了细胞级重染的配准精度，同时在ANHIR数据集上也表现出色。该方法不需要对新数据集进行微调，并可直接用于其他类型的显微镜图像。该方法已集成到DeeperHistReg框架中，可供其他人直接使用，以在任何所需的金字塔级别上对WSIs进行配准、变换和保存。该方法对WSI的配准是一个重要的贡献，推动了数字病理学领域的发展。

RegWSI:使用深度特征和基于强度的方法的全切片图像配准：ACROBAT 2023挑战赛获胜者