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Kidney Tools and Resources

The software for managing the digital kidney was made available with tremendous encouragement and help from staff at the Human Genetics Unit, Western General Hospital led by Professor Richard Baldock and Dr Duncan Davidson. In particular, the original sections were prepared by Allyson Ross, the digital manipulations were done by Dr Jianguo Rao and Liz Graham and the JAtlas software is the work of Dr Guangjie Feng. The kidney was from a 17.5 day mouse embryo, close to term. The sections were 2 microns.

The development of these tools for teaching was the work of Anna Goodall, a year 2 Vet student. In a short summer project, Anna created much of the output shown here.
Graham Pettigrew (


Kidney Movies

The JAtlas viewer allows you to relate 2-dimensional sections through a kidney to the 3-dimensional object. The tutorial shows how the viewer is used to study the kidney. You require headphones for the soundtrack on the tutorial.

'Using JAtlas' - Movie Tutorial (Movie of JAtlas features)
'Using JAtlas' - Instructions (Word document with pictures)

Try the Movie tutorial first as an introduction. To use the viewer yourself, you first need to load a data file from the section below. These data files should be downloaded into 'C:\Workspace' (see Datafiles below). Once you have a datafile to look at, you can open the JAtlas viewer using this link and use the file menu to navigate to your data file.
Launch the JAtlas Viewer
(requires Java3D and Javahelp components and appropriate data file)

In these 'painted' movies, the kidney appears grey on a light background and particular internal structures have been painted.

These movies are accompanied by labelled stills of chosen orientations such as those shown here. Use the JAtlas viewer to relate 2D painted sections to this 3D appearance.

JAtlas Data Files
Kidney Movie Files

Click on the datafile that you wish and save in C:\Workspace. Select the zip file and extract. When you open JAtlas you should navigate to the extracted datafile folder and find the datafile with the extension.wlz
Kidney (high-resolution) (large file,takes a while)
Kidney (low-resolution)

This powerpoint gives an introduction to the high resolution sections and the features that should be identified.
Viewing the Sections

Kidney - Regions of nephron 1
Kidney - Regions of nephron 2
Kidney - cortical and JM nephrons

CAL objects

(require Authorware webplayer)

Water recovery and urine concentration
Structure and function in the nephron
The concept of clearance

Get Authorware Web Player

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