Volume Planes

December 6, 2006

The volume planes dialog provides a slider to control which z-plane of a volume data set to display with gray-scale rendering. The term z-plane means a plane perpendicular to the data z axis. The dialog is displayed using menu entry

The slider controls the volume currently shown in the volume viewer dialog. It switches the display mode to "solid" and sets the subregion for the data set to include just a single plane. The slider value indicates the integer plane number with values starting at 0.

Brightness

The brightness of the displayed plane is controlled by the yellow curve shown on the volume data histogram in the Volume Viewer dialog. Move the nodes of the yellow curve to set the brightness (height of curve) for each data value.

Show sequence of planes

Pressing the Play button shows the volume planes one by one in order as fast as possible. When the last plane is reached it continues showing planes in the reverse direction (decreasing z). The play button is renamed to Stop after it is pressed.

The play button can be used in conjunction with the Chimera Movie Recorder tool (menu entry Tools / Utilities / Movie Recorder) to create a movie that shows the planes in sequence.

Show full-size plane

Pressing the Full button shows the current plane at full size. This is useful if the volume dialog crop feature previously reduced the width and height of the displayed plane.

Faster display of planes

To achieve faster switching between planes you can set the step size in the volume dialog to show less than full resolution (e.g. 2 2 2 to show every other data point along each axis). Even when using this subsampling the volume planes z slider allows display of every z-plane -- only the x and y dimensions are subsampled.

You can select a rectangular subregion of a plane to display using the volume viewer subregion selection feature. Moving the plane slider will then only show the selected subregion.

Limitations

Only z-planes. The dialog can only display z-planes. The code could easily be adapted to display planes perpendicular to x or y data axes. It could not easily be adapted to display planes that are not perpendicular to one of the three data axes.

One slider. Only one copy of the slider dialog can be shown. It always acts on the volume data currently show in the volume viewer dialog.

History

November 29, 2006.
Developed plane display dialog for viewing electron microscope tomography data.