title: Neurite analyzer: An original Fiji plugin for quantification of neuritogenesis in two-dimensional images.
abstract: In life sciences, there is a growing need for new informatics tools designed to provide automated solutions in order to analyze big amounts of images obtained from high-throughput imaging systems. Among the most widely used assays in neurotoxicity, endocrinology and brain diseases, the neurite outgrowth assay is popular.
  
  
  
  Cell-to-cell quantification of the main morphological features of neurite outgrowth assays remains very challenging. Here, we provide a new pipeline developed on Fiji software for analysis of series of two-dimensional images. It allows the automated analysis of most of these features.
  
  
  
  We tested the accuracy and usefulness of the software by confirming the effects of estradiol and hypoxia on in vitro neuronal differentiation, previously published by different authors with manual analysis methods. With this new method, we highlighted original interesting data.
  
  
  
  The innovation brought by this plugin lies in the fact that it can process multiple images at the same time, in order to obtain: the number of nuclei, the number of neurites, the length of neurites, the number of neurites junctions, the number of neurites branches, the length of each branch, the position of the branch in the image, the angle of each branch, but also the area of each cell and the number of neurites per cell.
  
  
  
  This plugin is easy to use, highly sensitive, and allows the experimenter to acquire ready-to-use data coming from a vast amount of images.
authors.affiliation: Transcription, Environment and Cancer Group, Institute of Research in Environmental and Occupational Health (IRSET), INSERM, Rennes, France.
authors.forename: Alexis J
authors.initials: AJ
authors.lastname: Haas
authors.affiliation: Biogenouest, Bio-imaging axis, Saint-Gilles, France; Microscopy Rennes Imaging Center (MRIC), Biosit - UMS CNRS 3480/US INSERM 018, University of Rennes 1, Rennes, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Prigent
authors.affiliation: Microscopy Rennes Imaging Center (MRIC), Biosit - UMS CNRS 3480/US INSERM 018, University of Rennes 1, Rennes, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Dutertre
authors.affiliation: Transcription, Environment and Cancer Group, Institute of Research in Environmental and Occupational Health (IRSET), INSERM, Rennes, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Le Dréan
authors.affiliation: Transcription, Environment and Cancer Group, Institute of Research in Environmental and Occupational Health (IRSET), INSERM, Rennes, France. Electronic address: ylepage@univ-rennes1.fr.
authors.forename: Yann
authors.initials: Y
authors.lastname: Le Page
mesh_terms: D000818:Animals; D015687:Cell Hypoxia / Q000502:physiology; D004958:Estradiol / Q000494:pharmacology; D047628:Estrogen Receptor alpha / Q000235:genetics / Q000378:metabolism; D004967:Estrogens / Q000494:pharmacology; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007150:Immunohistochemistry / Q000379:methods; D008853:Microscopy / Q000379:methods*; D020932:Nerve Growth Factor / Q000494:pharmacology; D016501:Neurites / Q000187:drug effects / Q000502:physiology; D055495:Neurogenesis / Q000187:drug effects / Q000502:physiology; D000071446:Neuronal Outgrowth / Q000187:drug effects / Q000502:physiology; D016716:PC12 Cells; D010363:Pattern Recognition, Automated / Q000379:methods*; D051381:Rats; D012984:Software
chemical_list: D047628:Estrogen Receptor alpha; D004967:Estrogens; D004958:Estradiol; D020932:Nerve Growth Factor
keywords: Automated neurite tracing; Fluorescence image analysis; High-content assay; Neurite outgrowth assay