Introduction to Annotation

From Endrov

Contents

Types of annotation

There are several types of annotation. The most versatile ones are listed below:

Lineage (branching-merging processes)

If you want to trace particles, be it cells or anything else, this is the plugin. Particles can divide and merge over time. In addition, time-varying properties can be associated with each particle. It has been used to model C. elegans embryogenesis with all gene expressions.

Network

Spatial networks can model connections between neurons and vascular systems. These can change over time and need not be a tree structure but there can also be loops.

Your own type of annotation

Sometimes it is not sufficient to reuse existing annotation models. Many projects would benefit from having their own type of annotation.

Endrov is a very modular system, making it not too difficult to add your own type of annotation. You need to know Java however, and to be able to render it in 3D (which is optional), you need to know a tiny bit of OpenGL. Adding a new type can be as little as one day of work but it depends heavily on how much functionality is needed. Endrov takes care of storing the data, be it in a file or in a database.