title: 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 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.
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Hernán
authors.identifier: http://orcid.org/0000-0002-9578-2556
authors.initials: H
authors.lastname: Morales-Navarrete
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Fabián
authors.initials: F
authors.lastname: Segovia-Miranda
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Piotr
authors.initials: P
authors.lastname: Klukowski
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Kirstin
authors.initials: K
authors.lastname: Meyer
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.|Rohto Pharmaceutical, Tokyo, Japan.
authors.forename: Hidenori
authors.initials: H
authors.lastname: Nonaka
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Marsico
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Chernykh
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Kalaidzidis
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Marino
authors.initials: M
authors.lastname: Zerial
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.|Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.
authors.forename: Yannis
authors.initials: Y
authors.lastname: Kalaidzidis
mesh_terms: D000818:Animals; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008099:Liver / Q000033:anatomy & histology; D008810:Mice, Inbred C57BL; D008853:Microscopy / Q000379:methods*; D061848:Optical Imaging / Q000379:methods*
keywords: 3D tissue geometrical model; computational biology; developmental biology; image analysis; mouse; stem cells; systems biology