|ZFIN ID: ZDB-PUB-131119-17|
|Source:||Bioinformatics (Oxford, England) 30(5): 726-33 (Journal)|
|Registered Authors:||Mikut, Ralf, Rastegar, Sepand, Shahid, Maryam, Strähle, Uwe, Takamiya, Masanari, Yang, Lixin|
|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/.