Abstract
The kidney is the organ responsible for blood filtration and is supplied with blood independently of its oxygen demand. This project was embedded in an overarching research initiative to investigate the properties and behavior of oxygen distribution of the kidney and its effects on oxygen-dependent mechanisms. Computational modeling of oxygen transport and distribution in the murine kidney requires detailed three-dimensional (3D) structural data of blood vessels, the main oxygen suppliers, and tubules, the main oxygen consumers. In order to provide these data on the whole kidney level, vascular casting protocols for X-ray microcomputed tomography imaging were developed. Mouse kidneys were subsequently imaged at synchrotron radiation facilities to acquire vascular and tubular structure datasets with full capillary resolution. Image processing and segmentation was performed on the resulting terabyte-scale dataset using high performance computing clusters, building the first 3D atlas of the vascular and tubular structure of a whole mouse kidney.
To make the process more widely accessible, a cross-linkable, polymeric X-ray contrast agent was developed and used for combined vascular and tubular imaging with widely available laboratory X ray source micro-CT equipment, which was previously reserved to synchrotron radiation facilities. Vascular and tubular structures were segmented in a simplified workflow based on free software and workstation-grade hardware.
Kuo, Willy