A novel method for identifying a graph-based representation of 3-D microvascular networks from fluorescence microscopy image stacks

Sepideh Almasi*, Xiaoyin Xu, Ayal Ben-Zvi, Baptiste Lacoste, Chenghua Gu, Eric L. Miller

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


A novel approach to determine the global topological structure of a microvasculature network from noisy and low-resolution fluorescence microscopy data that does not require the detailed segmentation of the vessel structure is proposed here. The method is most appropriate for problems where the tortuosity of the network is relatively low and proceeds by directly computing a piecewise linear approximation to the vasculature skeleton through the construction of a graph in three dimensions whose edges represent the skeletal approximation and vertices are located at Critical Points (CPs) on the microvasculature. The CPs are defined as vessel junctions or locations of relatively large curvature along the centerline of a vessel. Our method consists of two phases. First, we provide a CP detection technique that, for junctions in particular, does not require any a priori geometric information such as direction or degree. Second, connectivity between detected nodes is determined via the solution of a Binary Integer Program (BIP) whose variables determine whether a potential edge between nodes is or is not included in the final graph. The utility function in this problem reflects both intensity-based and structural information along the path connecting the two nodes. Qualitative and quantitative results confirm the usefulness and accuracy of this method. This approach provides a mean of correctly capturing the connectivity patterns in vessels that are missed by more traditional segmentation and binarization schemes because of imperfections in the images which manifest as dim or broken vessels.

Original languageAmerican English
Pages (from-to)208-223
Number of pages16
JournalMedical Image Analysis
Issue number1
StatePublished - 1 Feb 2015
Externally publishedYes

Bibliographical note

Funding Information:
The authors would like to thank the Enhanced Neuroimaging Core at Harvard NeuroDiscovery Center for helping with confocal imaging. We also thank Dr. Yutaka Yoshida from Cincinnati Childrens Hospital for providing the Plexin-D1-fGFP mouse. This work was supported by the National Science Foundation award 0958345 (S.A. and X.X.), the Goldenson postdoctoral fellowship (A.B.-Z.), the Harvard/MIT Joint Research Grants Program in Basic Neuroscience (X.X., B.L., and C.G.), United States. Finally, we thank the Editor as well as the Reviewers for their many helpful and constructive comments and suggestions that greatly improved this manuscript.

Publisher Copyright:
© 2014 Elsevier B.V.


  • Convex hull
  • Graph extraction
  • Junction detection
  • Microvascular network
  • Tubular structures


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