The 3D electron microscopy imaging is available using Electron Tomography (ET) or Serial Block Face Scanning Electron Microscopy (SB-EM). 

Electron tomography is TEM based method best suited for high resolution (~1-4 nm/pixel) imaging of relatively small areas. Typical dimensions of ET dataset is about 5.0 x 5.0 x 0.25 um.

Serial Block Face Scanning Electron Microscopy gives images with lower resolution (~10-20 nm/pixel in the XY plane; 25-50 nm/pixel in the Z plane) but allows to cover significantly larger areas. Typical dimensions of SB-EM dataset is 40 x 40 x 40 um.