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The alignment of tissue between histopathological whole-slide-images (WSI) is crucial for research and clinical applications. Advances in computing, deep learning, and availability of large WSI datasets have revolutionised WSI analysis. Therefore, the current state-of-the-art in WSI registration is unclear. To address this, we conducted the ACROBAT challenge, based on the largest WSI registration dataset to date, including 4,212 WSIs from 1,152 breast cancer patients. The challenge objective was to align WSIs of tissue that was stained with routine diagnostic immunohistochemistry to its H&E-stained counterpart. We compare the performance of eight WSI registration algorithms, including an investigation of the impact of different WSI properties and clinical covariates. We find that conceptually distinct WSI registration methods can lead to highly accurate registration performances and identify covariates that impact performances across methods. These results establish the current state-of-the-art in WSI registration and guide researchers in selecting and developing methods.

Low-rank and sparse decompositions and robust PCA (RPCA) are highly successful techniques in image processing and have recently found use in groupwise image registration. In this paper, we investigate the drawbacks of the most common RPCA-dissimi\-larity metric in image registration and derive an improved version. In particular, this new metric models low-rank requirements through explicit constraints instead of penalties and thus avoids the pitfalls of the established metric. Equipped with total variation regularization, we present a theoretically justified multilevel scheme based on first-order primal-dual optimization to solve the resulting non-parametric registration problem. As confirmed by numerical experiments, our metric especially lends itself to data involving recurring changes in object appearance and potential sparse perturbations. We numerically compare its peformance to a number of related approaches., 22 pages, 14 figures

Purpose: In digital histopathology, virtual multi-staining is important for diagnosis and biomarker research. Additionally, it provides accurate ground-truth for various deep-learning tasks. Virtual multi-staining can be obtained using different stains for consecutive sections or by re-staining the same section. Both approaches require image registration to compensate tissue deformations, but little attention has been devoted to comparing their accuracy. Approach: We compare variational image registration of consecutive and re-stained sections and analyze the effect of the image resolution which influences accuracy and required computational resources. We present a new hybrid dataset of re-stained and consecutive sections (HyReCo, 81 slide pairs, approx. 3000 landmarks) that we made publicly available and compare its image registration results to the automatic non-rigid histological image registration (ANHIR) challenge data (230 consecutive slide pairs). Results: We obtain a median landmark error after registration of 7.1 {\mu}m (HyReCo) and 16.0 {\mu}m (ANHIR) between consecutive sections. Between re-stained sections, the median registration error is 2.3 {\mu}m and 0.9 {\mu}m in the two subsets of the HyReCo dataset. We observe that deformable registration leads to lower landmark errors than affine registration in both cases, though the effect is smaller in re-stained sections. Conclusion: Deformable registration of consecutive and re-stained sections is a valuable tool for the joint analysis of different stains. Significance: While the registration of re-stained sections allows nucleus-level alignment which allows for a direct analysis of interacting biomarkers, consecutive sections only allow the transfer of region-level annotations. The latter can be achieved at low computational cost using coarser image resolutions., Comment: submitted, data available at https://dx.doi.org/10.21227/pzj5-bs61

Image registration, especially the quantification of image similarity, is an important task in image processing. Various approaches for the comparison of two images are discussed in the literature. However, although most of these approaches perform very well in a two image scenario, an extension to a multiple images scenario deserves attention. In this article, we discuss and compare registration methods for multiple images. Our key assumption is, that information about the singular values of a feature matrix of images can be used for alignment. We introduce, discuss and relate three recent approaches from the literature: the Schatten q-norm based SqN distance measure, a rank based approach, and a feature volume based approach. We also present results for typical applications such as dynamic image sequences or stacks of histological sections. Our results indicate that the SqN approach is in fact a suitable distance measure for image registration. Moreover, our examples also indicate that the results obtained by SqN are superior to those obtained by its competitors., 12 pages, 5 figures, accepted at the conference "Scale Space and Variational Methods" in Hofgeismar, Germany 2019

We present a 3-step registration pipeline for differently stained histological serial sections that consists of 1) a robust pre-alignment, 2) a parametric registration computed on coarse resolution images, and 3) an accurate nonlinear registration. In all three steps the NGF distance measure is minimized with respect to an increasingly flexible transformation. We apply the method in the ANHIR image registration challenge and evaluate its performance on the training data. The presented method is robust (error reduction in 99.6% of the cases), fast (runtime 4 seconds) and accurate (median relative target registration error 0.19%).

While deep learning has achieved significant advances in accuracy for medical image segmentation, its benefits for deformable image registration have so far remained limited to reduced computation times. Previous work has either focused on replacing the iterative optimization of distance and smoothness terms with CNN-layers or using supervised approaches driven by labels. Our method is the first to combine the complementary strengths of global semantic information (represented by segmentation labels) and local distance metrics that help align surrounding structures. We demonstrate significant higher Dice scores (of 86.5\%) for deformable cardiac image registration compared to classic registration (79.0\%) as well as label-driven deep learning frameworks (83.4\%)., Comment: Accepted at BVM Workshop 2019