Segmentation in Amira

Segmentation refers to the idea of ISOLATING and HIGHLIGHTING certain specific structures in a data matrix. It is what allows you to create separate surfaces for each structure within your data set and may be done manually or automatically depending on the type of material that you are segmenting.

Manual Segmentation

There are several tools within Amira which will allow you to manually segment pieces of your data set. They will be explained below.

Manual segmentation is best when the area you are segmenting is of similar colour contrast to surrounding structures (ie. muscles, tissue)

Paint Brush

The paint brush works very similarly to that of the paint brush in paint. You click to highlight sections of your slice (shown in orange-red colour)and hold control and click the left mouse button to