title: SAMA: A Method for 3D Morphological Analysis.
abstract: Three-dimensional (3D) culture models are critical tools for understanding tissue morphogenesis. A key requirement for their analysis is the ability to reconstruct the tissue into computational models that allow quantitative evaluation of the formed structures. Here, we present Software for Automated Morphological Analysis (SAMA), a method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed with minimum human intervention. SAMA allows quantitative analysis of key features of epithelial morphogenesis such as ductal elongation, branching and lumen formation that distinguish different hormonal treatments. SAMA is a user-friendly set of customized macros operated via FIJI (http://fiji.sc/Fiji), an open-source image analysis platform in combination with a set of functions in R (http://www.r-project.org/), an open-source program for statistical analysis. SAMA enables a rapid, exhaustive and quantitative 3D analysis of the shape of a population of structures in a 3D image. SAMA is cross-platform, licensed under the GPLv3 and available at http://montevil.theobio.org/content/sama.
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Tessie
authors.initials: T
authors.lastname: Paulose
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Maël
authors.initials: M
authors.lastname: Montévil
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Lucia
authors.initials: L
authors.lastname: Speroni
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Florent
authors.initials: F
authors.lastname: Cerruti
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Carlos
authors.initials: C
authors.lastname: Sonnenschein
authors.affiliation: Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Ana M
authors.initials: AM
authors.lastname: Soto
mesh_terms: D001331:Automation; D004847:Epithelial Cells / Q000166:cytology; D006801:Humans; D009024:Morphogenesis; D012984:Software