How are light sheet microscopy 3D images and their computed sections built up from stacks of 2D images?
According to their website dispim.org they are using registration software like the ImageJ Multiview-Reconstruction Plugin. Judging from the descriptions, this plugin uses the alignment of multiple points in the different angle images (like fluorescent beads that have been introduced to the medium or the cell nuclei) by rigid transformation and then deconvolves the 3D information using the point spread functions.

Knowing your optical system (microscope lenses etc.) you can calculate how the image of a point light source would look like in the image. This can be used to reversely calculate the actual position of your light source from the image and reconstruct an image without the distortions.

From that they get a volumetric image that can be projected into any coordinate system. I recommend watching the videos on the plugin page to get an idea how this works.