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Cited by 98Cell Image Analysis TechniquesMedical Image Segmentation TechniquesDigital Image Processing Techniques

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

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Morales-Navarrete, Hernán, Segovia-Miranda, Fabián, Klukowski, Piotr, Meyer, Kirstin, Nonaka, Hidenori, Marsico, Giovanni, Chernykh, Mikhail, Kalaidzidis, Alexander +2 more·2015·eLife
DOI 10.7554/elife.11214PMC PMC4764584
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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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  • In uninjured adult mouse livers, hepatocyte volume ranges from 3,126 μm3 to 10,606 μm3.

    “In uninjured adult mouse livers, hepatocyte volume ranges from 3,126 μm3 to 10,606 μm3.28”

    From Distinct hepatocyte identities in liver homeostasis and regeneration (2023) · cites this paper as [28]

    In Results, “New insights into liver tissue organization from the geometrical model” (page not provided), the paper reports 3,126 ± 1,302 and 10,606 ± 1,532 µm³ as mean volumes of two hepatocyte subpopulations measured in adult mice. They are not the minimum and maximum hepatocyte volumes, so describing them as the endpoints of a range misstates the finding. (LLM, conf=0.89)

    Experimental — accuracy not yet measured

  • Normal ploidies observed among adult mouse hepatocytes are diploid (2n), tetraploid (4n) and octaploid (8n); and 4n and 8n hepatocytes often have two nuclei (bi-nucleated).

    “Normal ploidies observed among adult mouse hepatocytes are diploid (2n), tetraploid (4n) and octaploid (8n); and 4n and 8n hepatocytes often have two nuclei (bi-nucleated).28”

    From Distinct hepatocyte identities in liver homeostasis and regeneration (2023) · cites this paper as [28]

  • In uninjured mouse livers, 2n mononuclear diploid and 2x2n binuclear tetraploid hepatocytes are more frequent in zone 1 and zone 3, while 2x4n binuclear octaploid hepatocytes are more frequent in zone 2, with 4n mononuclear hepatocytes distributed evenly across the lobule.

    “In uninjured mouse livers, there is some correlation between hepatocyte size and ploidy and their location within the lobule. 2n mononuclear diploid and 2x2n binuclear tetraploid hepatocytes are more frequent in zone 1 and zone 3, while 2x4n binuclear octaploid hepatocytes are more frequent in zone 2, with 4n mononuclear hepatocytes distributed evenly across the lobule.28”

    From Distinct hepatocyte identities in liver homeostasis and regeneration (2023) · cites this paper as [28]

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Cited by

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Authors
Morales-Navarrete, H., Segovia-Miranda, F., Klukowski, P., Meyer, K., Nonaka, H., Marsico, G., Chernykh, M., Kalaidzidis, A., Zerial, M., & Kalaidzidis, Y.
Affiliations
  • Max Planck Institute of Molecular Cell Biology and Genetics (DE)
  • Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
  • Rohto Pharmaceutical (Japan) (JP)
  • Lomonosov Moscow State University (RU)
Corresponding author
  • Zerial, Marino
  • Kalaidzidis, Yannis
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2015-12-17
Volume
4
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.11214
PMC
PMC4764584
OpenAlex
W2200588194
Cited by
98
References
4
Citations by year
2026: 6 · 2025: 6 · 2024: 7 · 2023: 13 · 2022: 4 · 2021: 8 · 2020: 14 · 2019: 14 · 2018: 9 · 2017: 11 · 2016: 6
FWCI
5.26
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Max Planck Institute for Plasma Physics (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
Funders
  • Bundesministerium für Bildung und Forschung
  • Max-Planck-Gesellschaft
  • Deutsche Forschungsgemeinschaft
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Digital Image Processing Techniques
Keywords
tissue structure, quantitative morphometry, image processing pipeline, liver tissue, hepatocyte zonation, liver sinusoids, bile canaliculi, cell shape analysis, lung tissue, kidney tissue, tissue organization
MeSH terms
Animals, Image Processing, Computer-Assisted, Liver, Mice, Inbred C57BL, Microscopy, Imaging, Three-Dimensional, Optical Imaging

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