Layer Tool

### Organising the display with the Layer Tool

Each graphical view renders a combination of the stored images according to the settings of that view's layer tool. You can think of the view as being the result of observing a stack of overlaid layers with different visibility, transparency, colour, etc., settings.

The top of the layer list (7) represents the uppermost layer of the rendered stack. Rendering is evaluated from the bottom up so layers higher up the list obscure those lower down.

The "Visibilty" checkbox (1) toggles whether or not a given layer is visible. You can also toggle this property by simply double-clicking on the relevant layer in the layer list. Each layer can be locked using the "Lock" checkbox (2). This property determines if a given layer can be edited or not. By default freshly loaded layers are locked, but new layers, those created with the "Create Mask" menu option, are un-locked by default and can be edited immediately. The "Transparency" slider (3) determines how the selected layer blends with the layers below it. A value of 1 makes any voxel above threshold completely obscure the same voxel in the layer below, while a value of 0 means this image makes no contribution to the rendered stack. The "Layer Up" (4), and "Layer Down" (5), buttons move the selected layer up or down the stack. Items lower down are obscured by those higher up the stack. The "Info" button (6) calls up the layer info dialog where you can get a fuller description of an images properties as well as modify some advanced options such as the look up table to be used. The "Layer List" box (7) indicates the order in which the layers will be evaluated along with visual feedback of that layers display settings. |

The layer marked with chevrons (8) to the right of it is the "main layer". This layer is the first one loaded during any given session and cannot be removed from the list as much of the viewer's display capabilities are determined from this layer's attributes.