A high-throughput analysis method to detect regions of interest and quantify zebrafish embryo images

Xiaoyan Xu, Xiaoyin Xu, Xin Huang, Weiming Xia, Shunren Xia

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1152-1159
Number of pages8
JournalJournal of Biomolecular Screening
Issue number9
StatePublished - Oct 2010


  • detect region of interest
  • high-throughput screening
  • image analysis
  • imaging
  • microscopy
  • morphological features
  • zebrafish

ASJC Scopus subject areas

  • Analytical Chemistry
  • Drug Discovery
  • Pharmacology
  • Biochemistry
  • Molecular Medicine
  • Biotechnology


Dive into the research topics of 'A high-throughput analysis method to detect regions of interest and quantify zebrafish embryo images'. Together they form a unique fingerprint.

Cite this