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

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 platform, we uncovered an unexpected zonation pattern of
hepatocytes with different size, nuclei and DNA content, thus revealing
new features of liver tissue organization. The pipeline also proved
effective to analyse lung and kidney tissue, demonstrating its generality
and robustness.