PUBLICATION
Zebrafish Vascular Quantification (ZVQ): a tool for quantification of three-dimensional zebrafish cerebrovascular architecture by automated image analysis
- Authors
- Kugler, E.C., Frost, J., Silva, V., Plant, K., Chhabria, K., Chico, T.J.A., Armitage, P.A.
- ID
- ZDB-PUB-220111-14
- Date
- 2022
- Source
- Development (Cambridge, England) 149(3): (Journal)
- Registered Authors
- Chico, Tim J.
- Keywords
- Angiogenesis, LSFM, Quantification, Registration, Vasculature
- MeSH Terms
-
- Animals
- Animals, Genetically Modified/growth & development
- Automation
- Brain/blood supply
- Cerebral Veins/diagnostic imaging*
- Cluster Analysis
- Embryo, Nonmammalian/blood supply
- Embryonic Development
- Image Processing, Computer-Assisted
- Imaging, Three-Dimensional/methods*
- User-Computer Interface
- Zebrafish/growth & development*
- PubMed
- 35005771 Full text @ Development
Citation
Kugler, E.C., Frost, J., Silva, V., Plant, K., Chhabria, K., Chico, T.J.A., Armitage, P.A. (2022) Zebrafish Vascular Quantification (ZVQ): a tool for quantification of three-dimensional zebrafish cerebrovascular architecture by automated image analysis. Development (Cambridge, England). 149(3):.
Abstract
Zebrafish transgenic lines and light sheet fluorescence microscopy allow in-depth insights into three-dimensional vascular development in vivo. However, quantification of the zebrafish cerebral vasculature in 3D remains highly challenging. Here, we describe and test an image analysis workflow for 3D quantification of the total or regional zebrafish brain vasculature, called zebrafish vasculature quantification "ZVQ". It provides the first landmark- or object-based vascular inter-sample registration of the zebrafish cerebral vasculature, producing Population Average Maps allowing rapid assessment of intra- and inter-group vascular anatomy. ZVQ also extracts a range of quantitative vascular parameters from a user-specified Region of Interest including volume, surface area, density, branching points, length, radius, and complexity. Application of ZVQ to thirteen experimental conditions, including embryonic development, pharmacological manipulations and morpholino induced gene knockdown, shows ZVQ is robust, allows extraction of biologically relevant information and quantification of vascular alteration, and can provide novel insights into vascular biology. To allow dissemination, the code for quantification, a graphical user interface, and workflow documentation are provided. Together, ZVQ provides the first open-source quantitative approach to assess the 3D cerebrovascular architecture in zebrafish.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping