title: Computerized image analysis for quantitative neuronal phenotyping in zebrafish.
abstract: An integrated microscope image analysis pipeline is developed for automatic analysis and quantification of phenotypes in zebrafish with altered expression of Alzheimer's disease (AD)-linked genes. We hypothesize that a slight impairment of neuronal integrity in a large number of zebrafish carrying the mutant genotype can be detected through the computerized image analysis method. Key functionalities of our zebrafish image processing pipeline include quantification of neuron loss in zebrafish embryos due to knockdown of AD-linked genes, automatic detection of defective somites, and quantitative measurement of gene expression levels in zebrafish with altered expression of AD-linked genes or treatment with a chemical compound. These quantitative measurements enable the archival of analyzed results and relevant meta-data. The structured database is organized for statistical analysis and data modeling to better understand neuronal integrity and phenotypic changes of zebrafish under different perturbations. Our results show that the computerized analysis is comparable to manual counting with equivalent accuracy and improved efficacy and consistency. Development of such an automated data analysis pipeline represents a significant step forward to achieve accurate and reproducible quantification of neuronal phenotypes in large scale or high-throughput zebrafish imaging studies.
authors.affiliation: Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, and Department of Radiology, Brigham and Women's Hospital, Boston, MA 02115, USA.
authors.forename: Tianming
authors.initials: T
authors.lastname: Liu
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Lu
authors.forename: Ye
authors.initials: Y
authors.lastname: Wang
authors.forename: William A
authors.initials: WA
authors.lastname: Campbell
authors.forename: Ling
authors.initials: L
authors.lastname: Huang
authors.forename: Jinmin
authors.initials: J
authors.lastname: Zhu
authors.forename: Weiming
authors.initials: W
authors.lastname: Xia
authors.forename: Stephen T C
authors.initials: ST
authors.lastname: Wong
mesh_terms: D000818:Animals; D002452:Cell Count / Q000379:methods; D004625:Embryo, Nonmammalian; D015870:Gene Expression / Q000502:physiology; D018507:Gene Expression Regulation, Developmental; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007150:Immunohistochemistry / Q000379:methods; D017403:In Situ Hybridization / Q000379:methods; D009474:Neurons / Q000145:classification / Q000166:cytology*; D016376:Oligonucleotides, Antisense; D012313:RNA / Q000008:administration & dosage; D015027:Zebrafish / Q000033:anatomy & histology* / Q000196:embryology; D029961:Zebrafish Proteins / Q000378:metabolism
chemical_list: D016376:Oligonucleotides, Antisense; D029961:Zebrafish Proteins; D012313:RNA