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
  • Cerebral Veins/diagnostic imaging*
  • Animals
  • Embryo, Nonmammalian/blood supply
  • Zebrafish/growth & development*
  • Imaging, Three-Dimensional/methods*
  • User-Computer Interface
  • Brain/blood supply
  • Embryonic Development
  • Cluster Analysis
  • Animals, Genetically Modified/growth & development
  • Automation
  • Image Processing, Computer-Assisted
(all 12)
PubMed
35005771 Full text @ Development
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.
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s916TgTransgenic Insertion
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    Sequence Targeting Reagents
    Target Reagent Reagent Type
    ccbe1MO1-ccbe1MRPHLNO
    dll4MO5-dll4MRPHLNO
    jag1aMO3-jag1aMRPHLNO
    jag1bMO1-jag1bMRPHLNO
    notch1bMO6-notch1bMRPHLNO
    tnnt2aMO1-tnnt2aMRPHLNO
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    Marker Marker Type Name
    mCherryEFGmCherry
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    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):.