title: Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish.
abstract: BACKGROUND
  To reliably assess the effects of unknown chemicals on the development of fluorescently labeled sensory-, moto- and interneuron populations in the spinal cord of zebrafish, automated data analysis is essential.
  
  
  RESULTS
  For the evaluation of a high-throughput screen of a large chemical library, we developed a new method for the automated extraction of quantitative information from green fluorescent protein (eGFP) and red fluorescent protein (RFP) labeled spinal cord neurons in double-transgenic zebrafish embryos. The methodology comprises region of interest detection, intensity profiling with reference comparison and neuron distribution histograms. All methods were validated on a manually evaluated pilot study using a Notch inhibitor dose-response experiment. The automated evaluation showed superior performance to manual investigation regarding time consumption, information detail and reproducibility.
  
  
  METHODS
  Being part of GNU General Public Licence (GNU-GPL) licensed open-source MATLAB toolbox Gait-CAD, an implementation of the presented methods is publicly available for download at http://sourceforge.net/projects/zebrafishimage/.
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany, Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany and Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Stegmaier
authors.forename: Maryam
authors.initials: M
authors.lastname: Shahid
authors.forename: Masanari
authors.initials: M
authors.lastname: Takamiya
authors.forename: Lixin
authors.initials: L
authors.lastname: Yang
authors.forename: Sepand
authors.initials: S
authors.lastname: Rastegar
authors.forename: Markus
authors.initials: M
authors.lastname: Reischl
authors.forename: Uwe
authors.initials: U
authors.lastname: Strähle
authors.forename: Ralf
authors.initials: R
authors.lastname: Mikut
mesh_terms: D000465:Algorithms; D000818:Animals; D030801:Animals, Genetically Modified; D005456:Fluorescent Dyes; D049452:Green Fluorescent Proteins / Q000032:analysis / Q000235:genetics; D057166:High-Throughput Screening Assays / Q000379:methods*; D008164:Luminescent Proteins / Q000032:analysis / Q000235:genetics; D009474:Neurons / Q000187:drug effects*; D015203:Reproducibility of Results; D013116:Spinal Cord / Q000166:cytology / Q000187:drug effects* / Q000196:embryology; D015027:Zebrafish / Q000196:embryology / Q000235:genetics*; D000097573:Red Fluorescent Protein
chemical_list: D005456:Fluorescent Dyes; D049452:Green Fluorescent Proteins; D008164:Luminescent Proteins; D000097573:Red Fluorescent Protein; C485184:enhanced green fluorescent protein