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Slice Viewer

A slice viewer is provided in the forward (XY) projection view. It allows for stepping through the dataset in the Z direction to view individual slices of the volume. The projection in the front view is updated to show the slice at each increment. The side and top views display an inverted line indicating the current Z position. This position is also displayed in the status bar at the bottom of the main window. The slice viewer is activated and deactivated by selecting View >> XY Slice Viewer from the main menu.

The Z position of the slice is controlled by using the keyboard. Press the Page Down key to increment the depth of the slice being viewed. This is similar to traversing the volume down the optical axis of the microscope. Press the Page Up key to decrement the Z position. The Home and End keys can be used to jump to the first and last slice respectively.

TIP: The slice position can also be adjusted with the move tool Move Tool by clicking and dragging on the slice line in either the side or bottom views.

The images below show the slice viewer from the forward, side, and 3D view respectively. Note that the Z position is always indicated in the status bar, and additionally as an inverted line in the side view.

Slice Viewer XY Slice Viewer ZY

The Z position is also displayed in the 3D viewer as a transparent plane. The intersection of this plane with the voxels of the dataset is displayed in an inverted color for enhanced visibility. See image below.

Slice Viewer 3D

In addition the above methods of controlling the position of the slice, you may also use the slice viewer control that is displayed in the 2D window. Switch to translate mode by selecting the move tool Move Tool from the tools panel of the main window or by selecting Edit >> Mode >> Translate from the main menu. Then simply click and drag on the knob of the control (see image below) and move up or down to control the position of the slice. This control is available in all the 2D viewing directions.

The slice viewer control in the 2D window.

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Send questions or comments to: alfredo.rodriguez@mssm.edu