SAMA: A Method for 3D Morphological Analysis

Tessie M Paulose (1) , Maël Montévil (2, 3, 1) , Lucia M Speroni (1) , Florent M Cerruti (1) , Carlos M Sonnenschein (4, 5, 1) , Ana Soto (4, 5, 1)

1 Department of Anatomy and Cell Biology Tufts University School of Medicine
2 IHPST - Institut d'Histoire et de Philosophie des Sciences et des Techniques
3 MSC - Matière et Systèmes Complexes
4 Centre Cavaillès
5 La République des savoirs : Lettres, Sciences, Philosophie

Three-dimensional (3D) culture models are critical tools for understanding tissue morpho-genesis. 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 epi-thelial 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.

Domaines: Autre [q-bio.OT]; Bio-informatique [q-bio.QM]; Morphogenèse; Sciences du Vivant [q-bio]

Tessie M Paulose, Maël Montévil, Lucia M Speroni, Florent M Cerruti, Carlos M Sonnenschein, et al.. SAMA: A Method for 3D Morphological Analysis. PLoS ONE, 2016, 11, ⟨10.1371/journal.pone.0153022⟩. ⟨hal-01438592⟩