PUBLICATION

Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish

Authors
Stegmaier, J., Shahid, M., Takamiya, M., Yang, L., Rastegar, S., Reischl, M., Strähle, U., and Mikut, R.
ID
ZDB-PUB-131119-17
Date
2014
Source
Bioinformatics (Oxford, England)   30(5): 726-33 (Journal)
Registered Authors
Mikut, Ralf, Rastegar, Sepand, Shahid, Maryam, Strähle, Uwe, Takamiya, Masanari, Yang, Lixin
Keywords
none
MeSH Terms
  • Algorithms
  • Animals
  • Animals, Genetically Modified
  • Fluorescent Dyes
  • Green Fluorescent Proteins/analysis
  • Green Fluorescent Proteins/genetics
  • High-Throughput Screening Assays/methods*
  • Luminescent Proteins/analysis
  • Luminescent Proteins/genetics
  • Neurons/drug effects*
  • Reproducibility of Results
  • Spinal Cord/cytology
  • Spinal Cord/drug effects*
  • Spinal Cord/embryology
  • Zebrafish/embryology
  • Zebrafish/genetics*
PubMed
24135262 Full text @ Bioinformatics
Abstract

Motivation: 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.

Availability and implementation: 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/.

Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping