An example of architectural design that includes the tree within the structure — very applicable to treehouse design. Almost all single tree, and many multi-tree treehouse designs have to deal with the issue of accommodating the tree trunk passing through the structure itself.
This is a hard problem because it is not possible to seal the roof to the tree bark — it grows, is spongy when wet, and cannot be cut or damaged without harming or killing the tree. This is an elegant solution: box the tree trunk in. The outcome is an open and airy interior feel, the advantages of natural sky-light illumination, and the tree trunk remains untouched and free to continue growing.
This solution does have a maximum life span, however, likely measured in decades before the tree out grows the pass-through. One also has to consider the amount of movement that the tree will likely endure swaying in high winds. And, glass tends to be quite heavy which is a something you want to minimize in a treehouse.
But the idea is great — and perhaps a bit of plexiglass or lexan would make it applicable to your next project.