A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture.

ABSTRACT: A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our

SUBMITTER: Morales-Navarrete H 

PROVIDER: S-EPMC4764584 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature