title: Segmentation and Quantitative Analysis of Epithelial Tissues.
abstract: Epithelia are tissues that regulate exchanges with the environment. They are very dynamic and can acquire virtually any shape; at the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the large number of cells composing an epithelium and the absence of informatics tools dedicated to epithelial analysis largely prevented tissue scale studies. Here we present Tissue Analyzer, a free tool that can be used to segment and analyze epithelial cells and monitor tissue dynamics.
authors.affiliation: IBDM-Institut de Biologie du Développement de Marseille, Campus de Luminy case 907, 13288, Marseille, cedex 9, France.
authors.forename: Benoit
authors.initials: B
authors.lastname: Aigouy
authors.affiliation: Graduate School of Life Sciences, Tohoku University, Aramaki Aoba 6-3, Sendai, 980-8578, Japan.
authors.forename: Daiki
authors.initials: D
authors.lastname: Umetsu
authors.affiliation: Max Planck Institute of Molecular Cell Biology, Pfotenhauerstrasse 108, 01307, Dresden, Germany. eaton@mpi-cbg.de.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Eaton
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D015820:Cadherins / Q000235:genetics / Q000378:metabolism; D058948:Cell Tracking / Q000379:methods; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D004331:Drosophila melanogaster / Q000378:metabolism / Q000648:ultrastructure; D004847:Epithelial Cells / Q000378:metabolism / Q000648:ultrastructure*; D004848:Epithelium / Q000378:metabolism / Q000648:ultrastructure*; D015870:Gene Expression; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007365:Intercellular Junctions / Q000378:metabolism / Q000648:ultrastructure*; D009024:Morphogenesis / Q000235:genetics; D010363:Pattern Recognition, Automated / Q000379:methods*; D012984:Software; D015027:Zebrafish / Q000033:anatomy & histology / Q000378:metabolism; D062826:Zonula Occludens-1 Protein / Q000235:genetics / Q000378:metabolism
chemical_list: D015415:Biomarkers; D015820:Cadherins; D029721:Drosophila Proteins; D062826:Zonula Occludens-1 Protein; C501889:shg protein, Drosophila
keywords: Cell tracking; Cells; Epithelia; Junctional remodeling; Junctions; Live imaging; Quantitative biology; Segmentation; Tissue Analyzer