2 First steps in amira

This chapter contains step-by-step tutorials illustrating the use of amira. The tutorials are almost independent of each other, so after reading the basics in the Getting Started section it is possible to follow each tutorial without knowing the others. If you go through all tutorials you will get a good survey of amira's basic features. In particular, these topics will be covered:

Getting started - the basics of amira
Reading images - how to read images
Visualizing 3D images - slices, isosurfaces, volume rendering
Image segmentation - segmentation of 3D image data
Surface reconstruction - surface reconstruction from 3D images
Grid generation - creating a tetrahedral grid from a triangular surface
Warping - how to work with landmark sets
3D image registration - how to register 3D image datasets
Alignment of 2D Physical Cross-Sections - how to reconstruct a 3D model
Vector fields - stream lines and other techniques
The DemoMaker module - creating animations with the DemoMaker module
Creating movie files - how to use the MovieMaker module
Using MATLAB - how to use the CalculusMatlab module

In all tutorials the steps to be performed by the user are marked by a dot. If you only want to get a quick idea how to work with amira you may skip the explanations between successive steps and just follow the instructions. But in order to get a deeper understanding you should refer to the text.

Note: If you want to visualize your own data, please first refer to Section 4.1. This section contains some general hints on how to import data sets into amira.