Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine

Alessia Candeo, Ilenia Sana, Eleonora Ferrari, Luigi Maiuri, Cosimo D'Andrea, Gianluca Valentini, Andrea Bassi

Research output: Contribution to journalArticlepeer-review


Light sheet fluorescence microscopy has proven to be a powerful tool to image fixed and chemically cleared samples, providing in depth and high resolution reconstructions of intact mouse organs. We applied light sheet microscopy to image the mouse intestine. We found that large portions of the sample can be readily visualized, assessing the organ status and highlighting the presence of regions with impaired morphology. Yet, three-dimensional (3-D) sectioning of the intestine leads to a large dataset that produces unnecessary storage and processing overload. We developed a routine that extracts the relevant information from a large image stack and provides quantitative analysis of the intestine morphology. This result was achieved by a three step procedure consisting of: (1) virtually unfold the 3-D reconstruction of the intestine; (2) observe it layer-by-layer; and (3) identify distinct villi and statistically analyze multiple samples belonging to different intestinal regions. Even if the procedure has been developed for the murine intestine, most of the underlying concepts have a general applicability.

Original languageEnglish
Article number056001
JournalJournal of Biomedical Optics
Issue number5
Publication statusPublished - May 31 2016


  • image processing
  • light sheet fluorescence microscopy
  • Three-dimensional microscopy

ASJC Scopus subject areas

  • Biomedical Engineering
  • Biomaterials
  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics


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