A framework for 3D vessel analysis using whole slide images of liver tissue sections

Abstract

Three-dimensional (3D) high resolution microscopic images have high potential for improving the understanding of both normal and disease processes where structural changes or spatial relationship of disease features are significant. In this paper, we develop a complete framework applicable to 3D pathology analytical imaging, with an application to whole slide images of sequential liver slices for 3D vessel structure analysis. The analysis workflow consists of image registration, segmentation, vessel cross-section association, interpolation, and volumetric rendering. To identify biologically-meaningful correspondence across adjacent slides, we formulate a similarity function for four association cases. The optimal solution is then obtained by constrained Integer Programming. We quantitatively and qualitatively compare our vessel reconstruction results with human annotations. Validation results indicate a satisfactory concordance as measured both by region-based and distance-based metrics. These results demonstrate a promising 3D vessel analysis framework for whole slide images of liver tissue sections.

Three‐dimensional reconstruction with serial whole‐mount sections of oral tongue squamous cell carcinoma: A preliminary study

“…As a novel emerging method, histopathological 3D reconstruction has been applied in the study of cell‐cell interaction in cancer, cancer cell invasion, and EMT marker, as well as vessel study . As for 3D observation of OTSCC, previous study on invasion front of OTSCC has been limited using limited parts of OTSCC samples, or only microinvasive OTSCC samples .…”

Histo-genomics: digital pathology at the forefront of precision medicine

“…Thus, image analysis of 2D microscopy was, until recently, subject to the same limitations of spatial information loss. The new advances in 3D microscopy allowed investigators to study disease-related biological structures in full authentic in situ 3D environments, which provided a wealth of information [101,102].…”

An integrative web-based software tool for multi-dimensional pathology whole-slide image analytics

“…A remote web application architecture allowing users to access a shared cluster of computational facilities addresses numerous computational challenges in pathology WSI analysis. The developed web application also enables the capability to create 3D tissue volumes from 2D serial tissue slides, including the incorporation of interdigitated biomarker sections [16][17][18][19]. Our online platform represents a substantial step forward for realizing the full potential of high-resolution integrative 3D tissue analytics by the research community [20][21][22][23].…”