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 .

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 on the C drive. Unzipping the file (right click and extract) reveals a folder containing the digital embryo as a file with the extension .wlz and an additional Anatomy folder.

1. Launch the JAtlas viewer using the link shown in the EEVeC page. Use ‘File open’ to navigate to your saved, extracted chick 60h folder and go into the folder to find and open a file called 60h.wlz.

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’. You can turn on and off a surface representation of the embryo in the 3-D rotation window using:

3D view/Show 3D surface

It is best to leave it turned off routinely for better computer performance.

Clicking once on the little horizontal lollipop to the left of ‘embryo’ on the Anatomy tree opens a menu of ‘painted domains’. A single click on each domain name will display the painted domain in the 3D window. 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. The following shows all the painted anatomy that is available on this embryo. Notice that the naming of the components is quite ‘loose’ and general. The domain called the heart for example includes both heart and major arteries.

Try rotating by dragging the mouse across the 3D window.

2. Viewing the ‘stack’ of 2D sections

Use the menu option ‘section’ to open the zx plane of cut. A new window opens which contains the central section of a series of sagittal sections of the embryo. We will call this the 2D window.

This section is numbered 0 in the box at the bottom right and is near to the midline.

At the moment the painted volumes are being shown and correspond in both the 3D window and the 2D window. These painted volumes slow down the handling of the images and are best turned off until a specific one is needed. Turn off both the 3D volumes and the 2D colouring using the 2D and 3D columns in the Anatomy key.

At the bottom of the screen is a section slider which reports which number of section is displayed. Sections run from -120 to +120 with the central section as zero. You can change section either by typing a negative or positive number into the box followed by return or by using the arrow keys on the keyboard to step through the sections.

Try doing this to see how the histology changes as you vary the position of the sagittal cut through the embryo.

3. Showing the plane of cut in the 3D window

One of the benefits of JAtlas is that it allows you to relate the 2D section to the 3D object. Use the Anatomy key to turn on just the CNS 3D volume and 2D painting.

In the 3D window, a coloured outline now indicates the plane of cut showing in the 2D window. You can adjust the size of the 3D window and you can use alt/mouse drag to change the size of the object. As you move through the section series, the position of this line changes. The coloured box at the top right of the 2D window corresponds to the colour of the relevant plane in the 3D window. Rotate the CNS volume in the 3D window so that the plane of cut is seen edge on. Use the section slider mechanism in the 2D window to see how the plane of cut moves in the 3D window.

The relationship between the section and the 3-D embryo can be emphasised by choosing ‘View texture’ in the 3D menuof the 2D window. This replaces the bounding outline with a representation of the section within the 3D window. It is heavy on memory and so should be turned on only when required.

Exercises

(a) Looking at the negative range of sections, try to identify the five vesicles of the brain, the optic vesicle, lens and optic stalk (optic nerve), the otic vesicle, the olfactory vesicle. Remember to consult the 3D window and the plane of cut when you are doing this.

(b) Turn off the 2D and 3D painting of the CNS and turn on the 2D and 3D painting of the heart and gut. Using the positive range of sections, try to identify the truncus arteriosus and its connections both to the ventricle and, in the floor of the pharynx, to the aortic arches leading to the dorsal aorta. The ventricle is thick-walled and muscular. The aortic arches pass through the branchial arches arranged around the pharynx.

(c) Turn off the 2D and 3D painting of the heart and gut and identify the section number shown on as Image A on the next page. With the help of the painted volumes (but remembering that their naming is rather general and you will need to label more specifically) try to identify as many features as possible and label the image accordingly

(d) Close the zx 2D window and use Section in the 3D window menu to choose the yz sections. (Choosing 'Show 3D surface' in 3D view menu will allow you to se ethe current plane of cut.) Identify the section number shown as Image B on the next page. With the help of the painted volumes try to identify as many features as possible and label the image accordingly

(e) Have a look at these movies:

chick 60h painted

chick 60h fluorescent

B Using the JAtlas viewer- THE 21 DAY PIG EMBRYO

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. Extracting 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 give an idea of the overall shape of the embryo. Turn off the 3D view and bounding box.

Exercises

(a)Choose View section xy. This is the original plane of sectioning and shows high quality detail. Scale the window to suit the screen. 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 volume reconstruction and its painted area in the section. Remember to remove the volumes from the anatomy key (using the 'see 3D' column in the anatomy key) once you have finished and before you move through the sections.

(b)Click on the pointer in the section slider and move through the negative numbered sections

Look for the connection of one limb bud and then the appearance of a second limb bud. Also observe the changing appearance of the lung buds (remember they are diverticula of the gut tube). Observe the splitting of the dorsal aorta around section -62. The olfactory epithelium lining the nasal pits becomes evident around section -65 to -95 (you can turn on nasal pit and cns in the anatomy tree to help you identify this). An optic vesicle comes into view around section -144 (again you can use ‘eye’ in Anatomy tree to help you identify that). 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 one arm of the split dorsal aorta and the heart. The best view of the aortic arches is with arterial volume on (using ‘3D' in the Anatomy key) and rotating the 3D window.

(c) Type in 0 to the bottom right box to return to the middle of the stack. Moving through the positive sections, the lung buds and the ventricle disappear around 30 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. In these sections the mesonephros is the dominant feature.

(d) Identify the section number shown on as Image C on the next page. With the help of the painted volumes try to identify as many features as possible and label the image accordingly

(e) Have a look at these movies

Pig 21 day sagittal painted

Pig 21 day transverse painted

Pig 21 day transverse unpainted

Appendix 1 - EMBRYOLOGY TOOLS AND RESOURCES
These are accessible via the graduate entry pages on EEVeC
This is the front page of Embryology tools and resources.
JAtlas / Embryo Movies

The JAtlas viewer allows you to relate 2-dimensional sections through an embryo to the 3-dimensional object. The tutorial shows how the viewer is used to study a chick embryo of 60 h. You require headphones for the soundtrack on the tutorial.
JAtlas viewer Tutorial Chick Embryo
Try the tutorial first as an introduction and then, to use the viewer yourself, download a datafile (see below) and then click on the ‘Launch the JAtlas viewer’ below.
Launch the JAtlas Viewer (takes a few seconds)
(requires Java3D and Javahelp components)
Use the file menu to navigate to Local Disc C/workspace and find the ‘wlz’ file within the unzipped folder / Some of these movies are the direct fluorescent output from the optical tomography method. In these movies the embryo appears bright against a dark background. In the painted and surface movies, the embryo is shown grey on a light background and particular organ systems or surfaces have been painted.
These movies are accompanied by labelled stills of chosen orientations such as tthose shown here. Use the JAtlas viewer to relate 2D painted sections to this 3D appearance.
Snapshots of different movies

JAtlas Data Files

/ Chick Embryo Movie Files Pig Embryo Movie Files
Click on the datafile below that you wish and save in C:\Workspace. Double click the zip file, select the folder that appears and extract all files to C:\Workspace. You should now see in your workspace, the zipped folder (which can be deleted), and your extracted folder.
Chick 40h
Chick 50h
Chick 60h
Pig 21 day sagittal
Pig 21 day transverse
/ Chick 40h fluorescent view 1 Pig 21 day sagittal painted
Chick 40h fluorescent view 2 Pig 21 day transverse unpainted
Chick 40h painted Pig 21 day transverse painted
Chick 50h fluorescent
Chick 50h surfaces
Chick 50h painted
Chick 60h fluorescent
Chick 60h painted
CAL objects
(require Authorware)
Embryonic Circulation
Formation of body folds
Segmentation
Pig embryo - sagittal sections
Pig embryo - transverse sections