I am attempting to create a 3D model of the surface of a leaf with enough detail to see stomata -- in a format such as .stl or .obj which could be edited and manipulated as a 3D mesh in any 3D editing program like Maya or Blender.

My first idea was to use Scanning Electron Microscopy to take many images at an angle (not directly above) in a 360 degree fashion around the area of the leaf focused on and use a photogrammetry program such as 123D catch to produce a 3D model from these images. The issue I've come up against with this is that without Low Temp SEM (I don't have access to cryoSEM, just regular SEM) capabilities the leaf would have to be dehydrated. Unfortunately, none of the chemical preservation methods I've come across preserve leaf structures to a satisfying degree. The surface of the leaf ends up looking deflated and deformed.

A friend suggested I consider laser confocal microscopy, which can be used to create "z stacks" of images that can be viewed as a 3D image in a special program. He was unaware if there was a way to then produce a 3D mesh file from this data though ~ such as a .stl or .obj that could be imported into 3D modeling software and manipulated.

Anyone know if z stacks can be converted to 3D models? Or know of other microscopy methods that could be used to create a 3D model of a microscopic object?