An end-to-end pipeline for 3D slide-wise multi-stain renal pathology registration

Peize Li; Ruining Deng; Yuankai Huo

doi:10.1117/12.2654542

6 April 2023 An end-to-end pipeline for 3D slide-wise multi-stain renal pathology registration

Peize Li, Ruining Deng, Yuankai Huo

Proceedings Volume 12471, Medical Imaging 2023: Digital and Computational Pathology; 124710F (2023) https://doi.org/10.1117/12.2654542
Event: SPIE Medical Imaging, 2023, San Diego, California, United States

Abstract

Tissue examination and quantification in a 3D context on serial section whole slide images (WSIs) were labor-intensive 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.

Conference Presentation

Citation Download Citation

Peize Li, Ruining Deng, and Yuankai Huo "An end-to-end pipeline for 3D slide-wise multi-stain renal pathology registration", Proc. SPIE 12471, Medical Imaging 2023: Digital and Computational Pathology, 124710F (6 April 2023); https://doi.org/10.1117/12.2654542

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