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High resolution 3D functional anatomy database of the kidney


Kuo, Willy. High resolution 3D functional anatomy database of the kidney. 2019, University of Zurich, Faculty of Science.

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.

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.

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Additional indexing

Item Type:Dissertation (cumulative)
Referees:Kurtcuoglu Vartan, Müller Bert, Wenger Roland H, Hieber Simone
Communities & Collections:04 Faculty of Medicine > Institute of Physiology
07 Faculty of Science > Institute of Physiology

UZH Dissertations
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Uncontrolled Keywords:Imaging, Kidney, X-ray tomography, Kidney disease, Synchrotron, Oxygen, Vasculature, Microscopy
Language:English
Place of Publication:Zürich
Date:22 August 2019
Deposited On:19 Mar 2021 15:46
Last Modified:19 Mar 2021 16:39
Publisher:Universität Zürich
Number of Pages:133
OA Status:Green
Project Information:
  • : FunderSNSF
  • : Grant ID205321_153523
  • : Project TitleHigh Resolution 3D Functional Anatomy Database of the Kidney
  • : Project Websitehttp://p3.snf.ch/project-153523
  • : FunderSNSF
  • : Grant ID51NF40-158771
  • : Project TitleNCCR Kidney.CH: Kidney Control of Homeostasis (phase II)
  • : Project Websitehttp://p3.snf.ch/project-158771
  • Content: Published Version