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 3dimensions 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. This picture 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.