Automated phenotype pattern recognition of zebrafish for high-throughput screening.
Over the last years, the zebrafish (Danio rerio) has become a key model organism in genetic and chemical screenings. A growing number of experiments and an expanding interest in zebrafish research makes it increasingly essential to automatize the distribution of embryos and larvae into standard microtiter plates or other sample holders for screening, often according to phenotypical features. Until now, such sorting processes have been carried out by manually handling the larvae and manual feature detection. Here, a prototype platform for image acquisition together with a classification software is presented. Zebrafish embryos and larvae and their features such as pigmentation are detected automatically from the image. Zebrafish of 4 different phenotypes can be classified through pattern recognition at 72 h post fertilization (hpf), allowing the software to classify an embryo into 2 distinct phenotypic classes: wild-type versus variant. The zebrafish phenotypes are classified with an accuracy of 79-99% without any user interaction. A description of the prototype platform and of the algorithms for image processing and pattern recognition is presented.
a Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen , Germany.
Mark
M
Schutera
b Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen , Germany.
Thomas
T
Dickmeis
b Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen , Germany.
Marina
M
Mione
b Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen , Germany.
Ravindra
R
Peravali
b Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology , Eggenstein-Leopoldshafen , Germany.
Daniel
D
Marcato
a Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen , Germany.
Markus
M
Reischl
a Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen , Germany.
Ralf
R
Mikut
a Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen , Germany.
Christian
C
Pylatiuk
D000465:Algorithms; D000818:Animals; D057166:High-Throughput Screening Assays; D007091:Image Processing, Computer-Assisted; D007814:Larva / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D010363:Pattern Recognition, Automated; D010641:Phenotype; D012984:Software; D015027:Zebrafish / Q000196:embryology* / Q000235:genetics*
feature detection; high-throughput screening; pattern recognition; support vector machine; zebrafish (Danio rerio)