ArticleeLife2015
A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture.
Article in eLife, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- NucVerse3D: generalizable 3D nuclear instance segmentation across heterogeneous microscopy modalities.Scientific reports · 2026Article
- Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics.Nature communications · 2026Article
- 3D reconstruction of human liver tissue at cellular resolution.Science advances · 2026Article
- Article
- Article
- Exploiting in silico modelling to enhance translation of liver cell therapies from bench to bedside.NPJ Regenerative medicine · 2024Review
- Shaping epithelial lumina under pressure.Biochemical Society transactions · 2024Review
- Phenotypic characterization of liver tissue heterogeneity through a next-generation 3D single-cell atlas.Scientific reports · 2024Article
- Heterogeneity in killing efficacy of individual effector CD8Proceedings. Biological sciences · 2023Article
- C1M2: a universal algorithm for 3D instance segmentation, annotation, and quantification of irregular cells.Science China. Life sciences · 2023Article
- Apical bulkheads accumulate as adaptive response to impaired bile flow in liver disease.EMBO reports · 2023Article
- Distinct hepatocyte identities in liver homeostasis and regeneration.JHEP reports : innovation in hepatology · 2023Review
- Survey of methods and principles in three-dimensional reconstruction from two-dimensional medical images.Visual computing for industry, biomedicine, and art · 2023Review
- A modular analysis of bile canalicular function and its implications for cholestasis.American journal of physiology. Gastrointestinal and liver physiology · 2023Review
- Effect of digital three-dimensional reconstruction technique combined with indocyanine green (ICG) excretion test for precision hepatectomy in primary liver cancer.American journal of translational research · 2023Article
- Quantification of Clonal Expansion of Hepatocytes in Normal and Injured Liver.Methods in molecular biology (Clifton, N.J.) · 2022Article
- An Improved Time- and Labor- Efficient Protocol for Mouse Primary Hepatocyte Isolation.Journal of visualized experiments : JoVE · 2021Article
- Review
- Anisotropic expansion of hepatocyte lumina enforced by apical bulkheads.The Journal of cell biology · 2021Article
- Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy.Nature communications · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.