Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs

Cell Rep Methods. 2023 Mar 17;3(3):100436. doi: 10.1016/j.crmeth.2023.100436. eCollection 2023 Mar 27.

Abstract

Light-sheet fluorescence microscopy (LSFM) can produce high-resolution tomograms of tissue vasculature with high accuracy. However, data processing and analysis is laborious due to the size of the datasets. Here, we introduce VesselExpress, an automated software that reliably analyzes six characteristic vascular network parameters including vessel diameter in LSFM data on average computing hardware. VesselExpress is ∼100 times faster than other existing vessel analysis tools, requires no user interaction, and integrates batch processing and parallelization. Employing an innovative dual Frangi filter approach, we show that obesity induces a large-scale modulation of brain vasculature in mice and that seven other major organs differ strongly in their 3D vascular makeup. Hence, VesselExpress transforms LSFM from an observational to an analytical working tool.

Keywords: 3D vasculature; high-throughput analysis; light-sheet fluorescence microscopy; open-source application.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / diagnostic imaging
  • Imaging, Three-Dimensional* / methods
  • Mice
  • Microscopy, Fluorescence / methods
  • Software*