Abstract Introduction Prevalently considered as the “gold-standard” for diagnosis of hepatic fibrosis and cirrhosis, the clinical liver needle biopsy is known to be subject to inadequate sampling and a high mis-sampling rate. However, quantifying such sampling bias has been difficult as generating a large number of needle biopsies from the same living patient is practically infeasible. We construct a three-dimension (3D) virtual liver tissue volume by spatially registered high resolution Whole Slide Images (WSIs) of serial liver tissue sections with a novel dynamic registration method. We further develop a Virtual Needle Biopsy Sampling (VNBS) method that mimics the needle biopsy sampling process. We apply the VNBS method to the reconstructed digital liver volume at different tissue locations and angles. Additionally, we quantify Collagen Proportionate Area (CPA) in all resulting virtual needle biopsies in 2D and 3D. Results The staging score of the center 2D longitudinal image plane from each 3D biopsy is used as the biopsy staging score, and the highest staging score of all sampled needle biopsies is the diagnostic staging score. The Mean Absolute Difference (MAD) in reference to the Scheuer and Ishak diagnostic staging scores are 0.22 and 1.00, respectively. The absolute Scheuer staging score difference in 22.22% of sampled biopsies is 1. By the Ishak staging method, 55.56% and 22.22% of sampled biopsies present score difference 1 and 2, respectively. There are 4 (Scheuer) and 6 (Ishak) out of 18 3D virtual needle biopsies with intra-needle variations. Additionally, we find a positive correlation between CPA and fibrosis stages by Scheuer but not Ishak method. Overall, CPA measures suffer large intra- and inter-needle variations. Conclusions The developed virtual liver needle biopsy sampling pipeline provides a computational avenue for investigating needle biopsy sampling bias with 3D virtual tissue volumes. This method can be applied to other tissue-based disease diagnoses where the needle biopsy sampling bias substantially affects the diagnostic results.

Virtual Liver Needle Biopsy from Reconstructed Three-Dimensional Histopathological Images: Quantification of Sampling Error