Insert the CD-ROM into the CD drive on your computer. Open a terminal (xterm) window by selecting the option from the appropriate menu and at the Unix % prompt type:

MAPaint &

UNIX is case sensitive so make sure you type this exactly as it appears here so that the command will be recognised.

Press return and a window will appear entitled “MAPaint”

Select “File” and then "Theiler setup". In the "Get Filename Dialog" pop up window that appears, navigate to the "Models" folder on the CD-ROM. The "Theiler stage" menu within the "File" menu will now be activated.

Select “File” and then “Theiler Stage”. Select TS12 from this menu.

A window containing a wireframe model of your chosen embryo model will appear within the three-dimensional frame defines by MAPaint

Select “Anatomy” then “Embryo” and “Notochord” and finally “Notochord Domain”. This will appear in the model in red. The whole image can be rotated in 3D space.

The anatomy menu contains every term in the anatomical nomenclature. Anything ending in “domain” represents a structure that has been specifically defined and can be viewed in the selected model.

Select the “Domain” menu and choose the “Select” option. From the sub-options, select the blue domain.

From the “Anatomy and “Embryo” menus, select “mesenchyme”; “trunk mesenchyme”; “paraxial mesenchyme”; “somite” and finally “somite domain”. This will now be loaded into your image and appear in blue.

Select green and then add the rest of the somites (i.e. somites 1-4) to your model.

From the “View” menu, select the X-Y view, which will bring up the Section Viewer. Note that the notochord domain is marked on the image.

Use the distance slider to move through the x-y sections of the embryo model. The red square around the 3D wireframe model in the MAPaint window will define exactly where you are on the model.

Those domains displayed in the model may also be removed.

Ensure that you still have green selected by checking the menu (the circle to the left of the text should be depressed). From the “Domain” menu, deselect “display 3D domain” and the green somites will disappear in the 3D display.

Now, select the "View Direction" at the top of the section viewer. Are you looking at this section from the top, or the bottom?

You should be able to identify this by using the yellow arrow that will appear in the MAPaint window.

Click on the “Controls” box, located under the image and use the Pitch slider to rotate the view until you are looking at the sections from the other side. At this point, the Pitch should be 180º and the yellow arrow pointing upwards.

Move the distance bar to view the sections from this angle.

Each voxel is defined in this model, and the description of each, together with the 3D coordinates will appear in the text box above the image as regions are selected with the middle mouse button. Clicking on a blue domain in the section, for example, should bring up the description of the somites in the paraxial trunk mesenchyme.