An End-to-end Pipeline for 3D Slide-wise Multi-stain Renal Pathology Registration
This is an incremental improvement for renal pathology researchers, reducing labor in 3D tissue registration.
The authors tackled the problem of aligning multi-stain whole slide images for 3D tissue analysis by providing a Docker-based pipeline, proving their existing Map3D method works on multi-stain data and needle biopsy samples, with the tools made publicly available.
Tissue examination and quantification in a 3D context on serial section whole slide images (WSIs) were laborintensive and time-consuming tasks. Our previous study proposed a novel registration-based method (Map3D) to automatically align WSIs to the same physical space, reducing the human efforts of screening serial sections from WSIs. However, the registration performance of our Map3D method was only evaluated on single-stain WSIs with large-scale kidney tissue samples. In this paper, we provide a Docker for an end-to-end 3D slide-wise registration pipeline on needle biopsy serial sections in a multi-stain paradigm. The contribution of this study is three-fold: (1) We release a containerized Docker for an end-to-end multi-stain WSI registration. (2) We prove that the Map3D pipeline is capable of sectional registration from multi-stain WSI. (3) We verify that the Map3D pipeline can also be applied to needle biopsy tissue samples. The source code and the Docker have been made publicly available at https://github.com/hrlblab/Map3D.