title: Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine.
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.
authors.affiliation: Politecnico di Milano, Dipartimento di Fisica, piazza Leonardo da Vinci 32, 20133 Milano, Italy.
authors.forename: Alessia
authors.initials: A
authors.lastname: Candeo
authors.affiliation: European Institute for Research in Cystic Fibrosis, IERFC ONLUS Foundation, Ospedale San Raffaele, Via Olgettina, 58, 20132 Milano, Italy.
authors.forename: Ilenia
authors.initials: I
authors.lastname: Sana
authors.affiliation: European Institute for Research in Cystic Fibrosis, IERFC ONLUS Foundation, Ospedale San Raffaele, Via Olgettina, 58, 20132 Milano, Italy.
authors.forename: Eleonora
authors.initials: E
authors.lastname: Ferrari
authors.affiliation: European Institute for Research in Cystic Fibrosis, IERFC ONLUS Foundation, Ospedale San Raffaele, Via Olgettina, 58, 20132 Milano, ItalycUniversity of Piemonte Orientale, Department of Health Sciences, 28100 Novara, Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Maiuri
authors.affiliation: Politecnico di Milano, Dipartimento di Fisica, piazza Leonardo da Vinci 32, 20133 Milano, Italy.
authors.forename: Cosimo
authors.initials: C
authors.lastname: D'Andrea
authors.affiliation: Politecnico di Milano, Dipartimento di Fisica, piazza Leonardo da Vinci 32, 20133 Milano, Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Valentini
authors.affiliation: Politecnico di Milano, Dipartimento di Fisica, piazza Leonardo da Vinci 32, 20133 Milano, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Bassi
mesh_terms: D000818:Animals; D066264:Datasets as Topic; D021621:Imaging, Three-Dimensional / Q000295:instrumentation / Q000379:methods*; D007413:Intestinal Mucosa / Q000000981:diagnostic imaging; D007422:Intestines / Q000000981:diagnostic imaging*; D051379:Mice; D008856:Microscopy, Fluorescence