Difference between revisions of "Segmentation in Amira"
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==Making a Selection, and Creating a Material== | ==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. | + | 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. |
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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. When you originally highlight a section, it will appear as a red-orange colour. | 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. When you originally highlight a section, it will appear as a red-orange colour. | ||
Revision as of 17:57, 13 June 2011
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.
Contents
Interacting with Slice Data
The following explains how to interact with slices using your mouse and available buttons in the Amira Viewer window.
To Pan a given object either vertically or horizontally: Click and hold the tracker ball on the mouse and drag your slide to the desired location. This may also be achieved by clicking the pan button (top left of screen, 3rd button from left of screen, looks like a hand ontop of 4 arrows) and then clicking and dragging your slide.
To Move through sequential slices: roll your mouse tracker ball forward or backward to move through the data set
Interacting with 3D Data
The following explains how to interact with a constructed 3D model using buttons in the Amira Viewer window or your Mouse. This applies to both 3D view in segmentation and pool modes.
To Translate an object without altering its orientation: click and hold the tracker ball on the mouse and drag your slide to the desired location. This may also be achieved by clickign the pan button (top left of screen, 3rd button from left of screen, looks like a hand ontop of 4 arrows) and then clicking and dragging your slide.
To Zoom in our out: roll the tracker ball forward or backward or click the zoom button (top left of screen, 4th button from left of screen, looks like a white vertical double headed arrow) then clicking your 3D data set and moving your mouse forward or backwards.
To Rotate your 3D object in space: click the left mouse button and move your mouse to orient the object as desired. If this doesn't work, click the rotate button (top left of screen, 2nd button from left of screen, looks like 2 wrapped and intersecting arrows) then try clicking on your object again.
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. 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
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
