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Journal of Biomedical Optics • Open Access

Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine
Author(s): Alessia Candeo; Ilenia Sana; Eleonora Ferrari; Cosimo D’Andrea; Luigi Maiuri; Gianluca Valentini; Andrea Bassi

Paper Abstract

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.

Paper Details

Date Published: 2 May 2016
PDF: 8 pages
J. Biomed. Opt. 21(5) 056001 doi: 10.1117/1.JBO.21.5.056001
Published in: Journal of Biomedical Optics Volume 21, Issue 5
Show Author Affiliations
Alessia Candeo, Politecnico di Milano (Italy)
Ilenia Sana, European Institute for Research in Cystic Fibrosis (Italy)
Eleonora Ferrari, European Institute for Research in Cystic Fibrosis (Italy)
Cosimo D’Andrea, Politecnico di Milano (Italy)
Luigi Maiuri, European Institute for Research in Cystic Fibrosis (Italy)
Univ. degli Studi del Piemonte Orientale Amedeo Avogadro (Italy)
Gianluca Valentini, Politecnico di Milano (Italy)
Andrea Bassi, Politecnico di Milano (Italy)


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