Using the Volume Transformer

To launch the Volume Transformer, click on the 3D Tools tab in the Analysis Panel in Aivia and select the Volume Transformer from the 3D Tools toolbar. This will open the Volume Transformer interface and create or show an existing ortho plane while hiding any existing clipping planes.

Align the Plane with the Image

Select and drag the unidirectional red, green, and blue arrows to adjust the position of the alignment point; this can help ease the alignment process but will not affect the volume transformation. Select and drag the curved, double-sided red, green, and blue arrows to adjust the angle of the ortho plane; this will affect how the image is transformed. Align the plane so that it appears "flat" to the image. 

Reset the Ortho Plane

Click Reset  to revert the ortho plane to its initial state, which corresponds to no rotation of the image.

Use Extra Alignment Points

Add three more alignment points to help with aligning the ortho plane to the image by selecting Extra Alignment Points  in the expanded More Options section. These three yellow points are anchored to the ortho plane and may be translated along the X, Y, or Z axes. To translate any of the alignment points, hover over the alignment point and then click and drag one of the arrows extending outward from the point. While any of the three extra alignment points is being moved, the other two remain in the same spatial location, helping to define the ortho plane. However, if the original alignment point, which appears as a white cube, is selected and used to manipulate the ortho plane, the extra alignment points are not guaranteed to stay in the same spatial locations.

Show the Intersecting Plane

Select Show Intersecting Plane  in the expanded More Options section to clip away parts of the image and show only the section made but cutting the image with the ortho plane. 

Optimize Image Size

Select Optimize Image Size  before applying a transformation to trim blank space from the sides of the rotated image (see below). Note that optimizing the image size can make the transformation take longer.

Show a Preview

You may turn on a preview by clicking the expand icon  next to More Options and then selecting Preview  to get an idea of how the image will be rotated. While a preview is shown, the original image is hidden.

Select Image Channels to Transform

By default, the image channels that are visible are transformed, and those that are hidden are neither transformed nor included in the transformed image. Click on the expand icon  next to More Options and then on Channels to Process  to open a menu where image channels can be selected or deselected for transformation.

Choose a New Bottom Plane

To change what the bottom plane (XY plane that appears furthest away when an image is first put in 3D View) will be in the transformed image, click on the expand icon  next to More Options, then on the expand icon  next to Advanced, and finally on the Bottom drop-down menu . By default, the bottom plane is set to Auto, which means the bottom plane is chosen in order to minimize the length of the Z dimension in the transformed image. The bottom plane that will be used in the transformation has a bold white frame around it. You may designate any of the six surfaces of the image cube as the bottom plane.

Apply Transform

Click Apply Transform  to transform the image. The transformed image will be displayed in the Image Viewer once it has been created, and its thumbnail will appear in addition to that of the original image in the Image Explorer. The transformed image is NOT automatically saved.