Serial sections in electron microscopy offer a big challenge in 3D reconstruction. Proper Z-alignment has been a great barrier, making it necessary to do painstaking, time consuming alignment work. Serial sectioning and alignment belong to the past since the introduction by FEI company of the Helios dual beam combined milling device / SEM-scanner. This instrument produces series of electron micrographs, perfectly Z-aligned. The inset shows six of the 360 images included in this dataset (the Z-frame distance is an amazing 25 nm) (dendrite - magenta and axon - red segmented with i -mod)
This screams for 3D reconstruction. Fortunately, the open-source program imod is available (EM Dept, University of Colorado, Boulder, Co) to do the hard work. Just a snap of the finger compared with the rough old days of 3D EM reconstruction! The next three images are screendumps of the FEI dataset of which I 3D reconstructed with imod seceral segmented structures: dendrite, two axons.
if nothing happens: download movie here