Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs
Philippa Spangenberg, Nina Hagemann, Anthony Squire, Nils Förster, Sascha D. Krauß, Yachao Qi, Ayan Mohamud Yusuf, Jing Wang, Anika Grüneboom, Lennart Kowitz, Sebastian Korste, Matthias Totzeck, Zülal Cibir, Ali Ata Tuz, Vikramjeet Singh, Devon Siemes, Laura Struensee, Daniel R. Engel, Peter Ludewig, Luiza Martins Nascentes Melo, Iris Helfrich, Jianxu Chen, Matthias Gunzer, Dirk M. Hermann, Axel Mosig
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.