ZFIN ID: ZDB-PUB-131119-17
Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish
Stegmaier, J., Shahid, M., Takamiya, M., Yang, L., Rastegar, S., Reischl, M., Strähle, U., and Mikut, R.
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

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/.