Download Using the JAtlas viewer

USING THE JATLAS VIEWER AND USING THE GENE
EXPRESSION DATABASE
What is the JAtlas viewer?
This is a tool developed by the MRC Human Genetics Unit here in Edinburgh to
display a 3-dimensional embryo and show virtual sections through it
How do I get the digital embryos?
These can be obtained from the Embryology Learning tools page in EEVeC
https://www.eevec.vet.ed.ac.uk/index.asp .
Select Teaching tools and resources/Embryology/JAtlas. No log-in is required
Choose the one you wish to study (the following describes the 60h chick embryo)
and down-load it as a zipped file into your workspace. Unzipping the file reveals a
folder containing the digital embryo as a file with the extension .wlz and an
additional Anatomy folder.
How do I open the chick 60h embryo in JAtlas viewer?
From the same page on
EEVeC you can launch the
JAtlas viewer (it takes a little
while). Then use File/open
from the menu to navigate to
and load the digital embryo
.wlz file that you have
unzipped into your
workspace.
You should have two open
windows. The left is the
viewing tool for rotating the
3-D embryo or its domains. The right is the anatomy ‘tree’. For the 60h chick
embryo, you should also have a surface representation of it in the 3-D rotation
window These surface representations do take up memory and it is best to turn it
off. Drag across the screen to show how you can rotate the object and then use
the Show 3D menu to unclick both the bounding box and the 3D surface
How do I view the virtual sections through the chick 60h embryo?
1. The menu option ‘view section’ allows you to choose between three cutting
planes Choose the the zx plane (90,90,90) of the 60h
chick embryo.
A new section viewer window opens. Click on the section
slider near the bottom of this window (note that you are at
section 0). Repetitive clicking on the right arrow key on
your keyboard will move you through the sections in a
positive direction (don't click too fast as it can cause the
software to hang up). As you click through, the bottom
right number will change to show the section number.
You can always return quickly to a particular section by
typing the section number into the bottom right box
followed by return. This is a quick way, for example, of
returning to section 0 in the middle of the stack. Try it.
Exercise A Can you find this section?
You can move back through the sections using the left arrow on the keyboard.
When you go below zero, the slide numbers show as negative. As you do this,
observe the changing appearance of the Central Nervous System, in particular the
spinal cord. The embryo is an imperfect shape so that different regions of the
spinal cord appear on different sections.
Exercise B Observe the optic stalk, optic vesicle and lens appearing in the region
of the forebrain in the section range -45 to -85
2. We have ‘painted’ selected ‘domains’ of the embryo for you and these appear in
the Anatomy tree to the right of the 3-D rotation window. These domains are
loaded by single clicking on the little horizontal arm of ‘embryo’ and then similarly
with CNS. Double clicking on the final CNS colours the central nervous system on
the section and loads a surface representation of that domain.
You can change the colour of the domain from the default value using the
Anatomy key (click on colour box)
Exercise C Rotate the embryo in the 3D window and observe the structure of the
brain, optic vesicle, otic vesicle and some cranial nerves. Then turn painted
volume off by using delete in the Anatomy Key.
3. Choose view section xy (0,0,0) and yz (90,0,90). This opens two new sections
windows at right angles to the original xz (90,90,90) plane. Choose Show/
'intersection of views in this original section window
If you go to the xy window (0,0,0) and click on the section slider, you can move
through the sections as you have done before. By default, you will start at section
zero and the position of this section relative to zx (90,90,90) is shown as an
intersection line in the zx window with a colour corresponding to the colour in the
top right box of the xy window (yellow in examples above). As you click through
the sections in the xy window, the line in the zx window will move to show the
section postion. At any stage, you can choose an anatomy component and display
it as a painted volume to help you understand the relationship between the
sections and the object. But best to delete the volume when you are moving
through sections
Exercise D As you move through the negative sections in the xy (0,0,0) window,
you will get good views of the olfactory pits, the optic stalk and vesicle and the
lens. You will also see the relatively early stages of caudal development compared
to the rostral components. This is typical of the chick. Development proceeds
much faster rostrally than caudally. As you go through the positive sections, you
will see the pharynx, the truncus arteriosus and ventricle (and the point where
these two become continuous), the otic vesicle, the lung buds (sections 75-95)
and regions of the gut tube. Right at the dorsal end of the sections, you will see
the segmentation of the somites
Exercise E There are two other chick embryo data files (50h and 40h) that could
be investigated but perhaps the best thing to do is to look at their corresponding
movies at EEVeC/Teaching tools and resources/Embryology/Movies
Chick 40h fluorescent and painted movies
Chick 50h fluorescent and painted movies
How do I view the sections through the 21 day pig embryo?
The digital chick and pig embryos are fundamentally different in the ways in
which they were obtained. The chick embryos are obtained by a process of
optical tomography. They are relatively low resolution because of this method
of collection but the virtual sections through them produce equivalent quality
in any plane. The pig embryos are reconstructions from an actual series of
sections. When viewed in the plane of these original sections, they are of high
quality and good resolution. However, when viewed in different planes, the
quality is much poorer because of the imperfections and distortions in both the
sections themselves and their alignment.
Choose the datafile named 'pig 21 day transverse' and down-load it as a
zipped file into your workspace. Unzipping the file reveals a folder containing
the digital embryo as a file with the extension .wlz and an additional Anatomy
folder. Open the .wlz file in the JAtlas viewer. The 3D view that loads into the
3D window is not very informative but it does show the process of
reconstruction from the transverse sections that has been carried out. Turn off
the 3D view and bounding box.
1. Choose View section xy (0,0,0). This is the original plane of sectioning and
shows high quality detail.
Exercise F The default section 0 shows details of ventricle, liver,
mesonephros, forelimb bud, neural tube, gut tube, lung bud and dorsal aorta.
Try identifying these structures. As before, you can check whether your
identification is correct by choosing a particular domain on the anatomy tree
and observing both its 3D reconstruction and its painted area in the section.
Remember to delete the volumes from the anatomy tree once you have
finished and before you move through the sections
2. Click on the pointer in the section slider and move through the negative
numbered sections
Exercise G As you move, you will see the limb bud connection being made
(around section -12) and the second limb bud appearing around section -28.
Observe the splitting of the dorsal aorta around section -62. The olfactory
epithelium lining the olfactory pits becomes evident around section -65 to -95.
An optic vesicle comes into view around section -144. Aortic arches are
difficult to see in these sections but if you look at the series -153 to -160 you
will see an aortic arch connection forming between the dorsal aorta and the
heart. It might be best to turn the arterial volume on (Anatomy tree) in order to
see that. The joining of the laryngo-tracheal groove to the pharynx can be
seen around section -202 to -212.
Type in 0 to the bottom right box to return to the middle of the stack. Moving
through the positive sections, the ventricle disappears as the liver and
mesonephros become very prominent. Try now to follow the gut tube. The gut
tube expands into the stomach around section 50. The herniated gut tube can
be seen between sections 150 to 180.
Exercise H There is also a sagittal data file that could be investigated but
perhaps the best thing to do is to look at their corresponding movies at
Pig 21 day sagittal painted
Pig 21 day transverse painted
Pig 21 day transverse unpainted
What is the gene expression database?
The UK MRC Human Genetics Unit in Edinburgh has developed a digital
database (the Edinburgh Mouse Atlas Project) as a resource for spatially
mapped data such as in situ gene expression.
http://genex.hgu.mrc.ac.uk/
1. Choose Emage gene expression database, then choose web search
EMAGE/browse
2. Choose Search gene/protein. Enter Pax6 (this opens a complete listing of
the study of Pax6 expression at different stages and with different methods)
3. Scroll to EMAGE 361 and select by clicking
4. This is material we have looked at in the lecture. You can view the image,
view the movie which shows the context of the section studied in the 3D
embryo, view the probe information and the method of visualisation
A second portion of the database contains tools for viewing sections through
the reconstructed embryo. If you return to:
http://genex.hgu.mrc.ac.uk/
and choose 3D embryo anatomy atlas
1. Choose the Theiler stage 15 embryo
(you may need to adjust the level of the split top/bottom screens by dragging
at the interface)
2. Clicking on the view of the whole embryo give a section at that level
Sagittal, transverse or frontal sections can be chosen. This is very similar to
JAtlas
3. In the bottom window there are movies to play. Try the section movies
which animate a series of continuous sections in one chosen plane
Examples of detection of gene expression in Drosophila
embryos
Anterior pole
-Gal reporter
B
C
Horse radish peroxidase
conjugated to second
antibody
In-situ hybridisation
Questions:
1) These figures represent the pattern of expression of genes involved in
Drosophila body plan development. Different techniques have been
used to show the expression of these genes. Which are the gene types
represented in the panels?
2) Which defects in body plan development do you expect if the gene in
‘B’ is inactivated?