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This is the home of the Xglom - exploring glomeruli - the multimodal kidney image analysis application.

Our Vision: Deploy an integration and analysis pipeline that will enable high-throughput, multi-modal, multi-resolution characterisation of ex-vivo animal model kidneys by assembling and integrating digital volumetric data from nanoscopic, microscopic and mesascopic imaging instruments.

Project Summary

This project is funded through ANDS in collaboration with the Bertram Lab (Department of Anatomy and Developmental Biology at Monash University), Monash Biomedical Imaging (Monash Biomedical Imaging) and Monash eResearch Centre (MERC). The aims of the project are to enable high-throughput, multi-modal, multi-resolution characterisation of ex-vivo animal model kidneys, by assembling and integrating digital volumetric data from nanoscopic, microscopic and mesascopic imaging instruments. The application is called Xglom, an extensive and interactive MATLAB program for exploring and analysing 3D kidney images. Through a related activity, Magnetic Resonance (MR) images of ex-vivo mouse and rat kidneys will be acquired with the Monash Biomedical Imaging Agilent 9.4T animal MR scanner, and existing automatic MR image analysis software that makes a complete count of glomeruli in a whole kidney will be deployed on the Multi modal Australian ScienceS Imaging and Visualisation Environment (MASSIVE) cluster.  This work alone will immediately give Australian biomedical researchers the unfair advantage in the crucial, nascent field of the quantification of glomerular distribution and its relationship to nephron number and chronic kidney disease.


But we will go further: we will assemble a system that enables, for the first time, the same glomerular counting code to be applied to stacked optical microscopy images from the forthcoming state-of-the-art slide scanner in the Department of Anatomy and Developmental Biology at Monash University, thereby reducing or even eliminating the need for extremely time-consuming (and therefore expensive) manual stereological counting of glomeruli. We will complete our kidney image analysis system by extending it to deliver automated tomographic image reconstruction and glomerular distribution quantification of kidneys imaged with the Australian Synchrotron Imaging and Medical Beamline. In total, the proposed system will place Australian researchers and their international collaborators at the absolute forefront of ex-vivo kidney imaging and image analysis, perfectly placed to translate the work to in-vitro animal organs, and ultimately in-vivo animal models and then humans.

Xglom being run inside a virtual desktop on MASSIVE. Two contrast-enhanced rat kidneys were scanned in the Agilent 9.4T MR scanner and processed using the Xglom MR pipeline.

Xglom's virtual microscopy plugin GlomViewer being run inside a virtual desktop on MASSIVE. Ex-vivo human kidneys were sliced and scanned in in the Aperio scanner at the Histology Lab at Monash University. The GlomViewer application is interactive and allows the user to label and count glomeruli and then create a stereological profile of each glomeruli. 

Video Gallery

Advanced extraction of glomeruli in Xglom's MRI pipeline.  Rat kidneys (ex vivo) - MBI Agilent 9.4T small animal MRI - Cationic ferritin contrast 

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The video of Professor John Bertram  and Professor Gary Egan highlighting the value of the Xglom tool is now available on YouTube.
This video was produced by Rachel Zelada. The video production and editing was done by Dr. Steve Welsh.

 

This project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative.