An End-to-end Pipeline for 3D Slide-wise Multi-stain Renal Pathology
  Registration
Peize Li Ruining Deng Yuankai Huo
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.