A Toolkit For Analyzing 3D Architecture In The Renal Papilla

Three-dimensional architecture of collecting ducts (CD), loops of Henle (LH), and blood vessels in the renal papilla. Advanced florescent microscopy imaging technology allows the scientists to visualize the three-dimensional (3D) architecture of CD and LH, when investigating various renal disease models. However, the quantitative analysis on the 3D papilla florescent microscope images is challenging and unscalable with conventional manual analysis. In this study, we develop and disseminate an open-source toolkit to segment, trace, and analyze the CD and LH in papilla, based on neuTube [1], a prevalent neuro-tracking software.