Segmentation in Amira

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Revision as of 17:33, 15 June 2011 by Brewski (Talk | contribs) (Paint Brush File:paintbrush.jpg)

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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.




Link to: Amira Interface: 3D and Slice Data

Making a Selection, and Creating a Material

The images that you work with in Amira are formed voxels -- a 3D version of a pixel. Essentially each pixel from each slice that you add originally as a part of your data set is assigned a 3D point in space and becomes a 3D cube volume occupying the dimensions of that slice and the distance between that slice and the one next to it. These voxels may then be realigned to create other planes of data projection.


When you interact with a data set in segmentation mode, you are selecting voxels to eventually become part of a given material. Each time you highlight a section, you have the option of adding selected voxels into a created material through manually clicking the add button or pushing "a" on the keyboard. When you originally highlight a section, it will appear as a red-orange colour. This denotes the selection that you are currently interacting with using segmentation tools. This is NOT a saved section, and does not contribute to forming a material until it is added to that material. Clicking the add button will transfer this selection of voxels into a material file. Be sure that you have the appropriate material selected from the materials list before clicking add. Doing this will remove the red-orange colouring and will show an outline of your new material in a colour matching the box beside it's name. To change the colour of a material double click the coloured box next to its name, select a new colour from the graded scales or colour wheel and click apply.

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 erase part of a selection (orange-red).

The paint brush is the only tool which allows multiple separate highlights on the same page withough erasing previously highlighted (but not added) work. You may also use this tool in conjunction with other tools to further edit a selection that has been made but not yet added to a material.

Lasso Tool Lassotool.jpg

The Lasso Tool also works very similarly to that of the lasso in paint. Clicking and holding the left mouse button will allow you to draw a free-handed outline of a section. This outline will then be filled in automatically and once red-orange in colour, may be added to a material. To edit this newly selected area (still red-orange) click the paintbrush button and add or subtract voxels as listed above.

NOTE: You CANNOT deselect voxels in a red-orange area using the lasso -- you must use the paintbrush. In otherwords, If you have already selected an area (area 1) using the lasso, selecting another area (area 2) withough first adding area 1 first will cause deselection of area 1 and selection of area 2.

Automatic Segmentation

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