Using the JAtlas viewer
What is the JAtlas viewer?
This is a tool developed by the MRC Human Genetics Unit here in Edinburgh to display 3-dimensional embryos and show virtual sections through them. We will be using it to display a 3D digital kidney
How are the digital kidneys obtained?
These are prepared from an original set of 823 sections each of 2 m cut from the kidney from a 17.5 day mouse embryo. The entire kidney is a very large file and we will look at two sub-samples of it. The first is a low resolution view of 100 sections from roughly the middle of the kidney including the region where the calyx enters the ureter. In this reconstruction the ‘voxel’ (equivalent of a pixel in three dimensions) is cubic with dimensions 2 m by 2 m by 2 m. This will give you a view of the kidney as a whole and can be viewed in the xy plane (the plane of original sectioning) and also the xz and yz planes. The second reconstruction is a high resolution one of the same sections but with masked areas to reduce the file size and make it manageable for viewing. The higher resolution does mean that one can look at cellular detail in the xy plane but it also means that the ‘voxel’ is not cubic and the nephron appears squashed when viewed in 3-dimensions or in the xz or yz planes.
Use the low resolution file to obtain an overview of the internal structure of the kidney; Use the high resolution file to view some of the cellular detail
How do I get the digital kidney files?
The two different resolutions of kidney can be obtained from the Kidney Learning tools page in EEVeC (Body Systems 1, lecture database, Fluid homeostasis and the kidney). Choose the one you wish to study and down-load it as a zipped file into your workspace. Unzipping the file reveals a folder containing the digital kidney as a file with the extension .wlz.
How do I open the low resolution kidney in JAtlas viewer?
Again from the Embryology Learning tools page in EEVeC you can launch the JAtlas viewer. Then use File/open from the menu to navigate to your workspace and load the low resolution digital kidney .wlz file.
You should have two open windows. The left is the viewing tool for rotating the 3-D kidney or its domains (just drag on the window). The right is the anatomy ‘tree’. A crude surface view of the portion of the kidney is displayed in the 3D window. This shows the exit of the ureter and allows you to orient yourself when the domains are then loaded (see below). But the 3D kidney does obscure your view of subsequent regions (and also slows the response of the computer) so it is best to turn it off by un-clicking ‘show 3D surface’ in the 3D view menu once you have orientated yourself.
How do I view the kidney sections?
The menu option ‘view section’ allows you to choose between three cutting planes and you can open all three if you wish. But the best one is the xy plane since that is the plane of original sectioning. The other two planes reveal the imperfections in the ‘reconstruction’ (this is the procedure for aligning the individual histology sections).
The picture shows the xy window. At the bottom of the window is a section slider which reports which number of section is displayed. Sections run from -50 to + 50 with the central section as zero. You can change section either by typing a negative or positive number into the right side box followed by return, or by using the slider mechanism.
We have digitally ‘painted’ selected ‘domains’ of the kidney for you and these appear in the Anatomy tree to the right of the 3D rotation window. These domains are loaded by clicking on the little horizontal arm of, for example, ‘Regions of one nephron’ and then similarly with ‘Proximal tubule’. Double clicking on the final ‘Proximal tubule’ colours that domain of a nephron on the section and also loads a volume representation of that domain. Other domains can be similarly loaded. The opened domains are represented in a new window called the anatomy key. Using this key, the colour of a domain can be altered and domains can be removed or turned off. You can also resize the objects shown by using the ‘Alt’ key while dragging the mouse within the 3D window.Thispicture shows all the kidney anatomy that is available for this low resolution file.
You will see that a juxtamedullary nephron has been ‘painted’ at around 11 oclock in the orientation. The collecting duct is complex and links to many nephrons only one other of which has been painted, this time a cortical nephron. There is also a cluster of glomeruli around the painted nephron that have been painted to give some idea of their density within the kidney cortex
Having orientated yourself and having seen what areas have been painted, it is quite a good exercise to turn the 2D painting off in the Anatomy key and turn on the ‘Mouse click anatomy’ in the Show menu of the section window. Now, when a painted region is clicked, its nature will be reported in the feedback window and it will be painted. Try moving through the sections using the section slider mechanism and the left or right arrow keys on the keyboard and at each stage try to identify the nephron anatomy that appears and then check it by clicking on the region. Clicking on a different region removes the original painting
How does the 3-D rotation window integrate with the section viewer
The painted volumes have appeared in the 3-D rotation window in the same colour as they appear in the section viewer.
The relationship between the section and the 3-D embryo can be emphasised by choosing ‘View texture’ in the 3D menu in the section viewer window. This replaces the bounding box with a representation of the section within the 3D window. This section will change as the section slider is changed, although this is not a good way to move through the sections because the ‘View texture’ is heavy on memory and slows the process down markedly. Better to turn ‘View texture’ on only when you have navigated to a section of interest.
How do I view the high resolution kidney sections?
The high resolution kidney sections are contained in a separate downloadable zipped file which is dealt with in the same way as the low resolution file.
This picture shows one high resolution section in the section window on the left. To produce a manageable file size, most of the kidney has been masked. We are seeing the same nephron at 11 oclock that was painted in the low resolution reconstruction. The kidney capsule is at the top left and the calyx is at the bottom right. The zoom was set to 35% and you can adjust this to suit your screen. Most of the painted domains that are available are shown. The painted volumes in the right side window are, however, very flattened due to the non-cubic voxel dimensions. Both the display of the sections and of the volumes are heavy on memory and you will only be able to move satisfactorily through the sections if you turn all the 3D volumes off and even then the section slider is quite unresponsive. However, the histology resolution is impressive and you can see individual cells sharply defined.