The AutoCropImageFilter creates a new mitk::Image object as output. This image has a new SlicedGeometry3D that has the same orientation as the SlicedGeometry3D of the input image. The origin of the SlicedGeometry3D is corrected according to the cropped region.

However, the PlaneGeometries that are held within the SlicedGeometry3D are not correctly initialized.
These PlaneGeometries are created but not initialized with the necessary information. Thus, the resulting PlaneGeometries have an origin of (0,0,0) and a direction of (0,0,1) even if the cropped image is not aligned like this.

This problem can be fixed by initializeing the SlicedGeometry3D of the output image with correctly created and initialized PlaneGeometries.

This has not been noticed so far, as the resulting PlaneGeometries are not used in the ExtApp. Only the SlicedGeometry is evaluated.