The Edinburgh Mouse Atlas Project: School Tutorial - Defining Anatomy

To be able to enter textual data into a database it is important that any words or terms that are used  have only one meaning. Otherwise the information in the database may be inconsistent. The language used to describe the embryo consists of anatomical names so we have to define these and delineate, or identify, the named parts of the embryo in our models. This allows us to go from a text description to a spatial description and visa-versa. We call the process of delineating the parts of the embryo painting and use a program that allows us to paint in 3D directly. These two steps, naming the parts and painting the parts are shown below. This process allows us to delineate a set anatomical domains. These domains are stored in a database which can be accessed via the web.

This shows a snapshot of the database interface which allows the biologist to browse through the anatomy names. We have organised these names into a "tree". The tree is called a part-of hierarchy because each component of the tree is part of the higher level component. In this way the embryo is chopped up into smaller and smaller anatomical bits and bobs. Sometimes the tree is a "chainsaw" part, i.e. as if the whole part had been cut off along some dotted line such as the limb, in other places it is a "systems" part e.g. cardiovascular system which is all the arteries, veins and heart.

This is a picture of the paint program showing some anatomy being painted. The controls allow any view of the embryo to be displayed and the paint can be put onto any of them.

When the anatomy has been defined it can displayed using 3D rendering software which can also produce movies. There are more examples when you get to the example piccies and movies page