PUBLICATION
A high-throughput analysis method to detect regions of interest and quantify zebrafish embryo images
- Authors
- Xu, X., Xu, X., Huang, X., Xia, W., and Xia, S.
- ID
- ZDB-PUB-101018-5
- Date
- 2010
- Source
- Journal of Biomolecular Screening 15(9): 1152-1159 (Journal)
- Registered Authors
- Xia, Weiming
- Keywords
- zebrafish, high-throughput screening, image analysis, detect region of interest, morphological features, microscopy, imaging
- MeSH Terms
-
- Algorithms
- Animals
- Dimethyl Sulfoxide/pharmacology
- Embryo, Nonmammalian/anatomy & histology*
- Embryo, Nonmammalian/drug effects
- High-Throughput Screening Assays/methods*
- Imaging, Three-Dimensional/methods*
- Pigments, Biological/metabolism
- Zebrafish/embryology*
- PubMed
- 20930217 Full text @ J. Biomol. Screen.
Citation
Xu, X., Xu, X., Huang, X., Xia, W., and Xia, S. (2010) A high-throughput analysis method to detect regions of interest and quantify zebrafish embryo images. Journal of Biomolecular Screening. 15(9):1152-1159.
Abstract
Zebrafish is widely used to understand neural development and model various neurodegenerative diseases. Zebrafish embryos are optically transparent, have a short development period, and can be kept alive in microplates for days, making them amenable to high-throughput microscopic imaging. As a result of high-throughput experiments, a large number of images can be generated in a single experiment, posing a challenge to researchers to analyze them efficiently and quantitatively. In this work, we develop an image processing focused on detecting and quantifying pigments in zebrafish embryos. The algorithm automatically detects a region of interest (ROI) enclosing an area around the pigments and then segment the pigments for quantification. In this process, the algorithm identifies the head and torso at first, and then finds the boundaries corresponding to the back and abdomen by taking advantage of a priori information about the anatomy of zebrafish embryos. The method is robust in terms that it can detect and quantify pigments even when the embryos have different orientations and curvatures. We used real data to demonstrate the performance of the method to extract phenotypic information from zebrafish embryo images and compared its results with manual analysis for verification.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping