Haberthur et al wanted to image gold particles (200 and 700 nm) in rat lungs. In order to do so they performed vascular perfusion on the tissue samples and shaped them with a watchmakers lathe. They then did x-ray tomographic microscopy at a wavelength of 11.5 kilo electron volts, yielding the pixel resolution of 350 nm by 350 nm by 350 nm. This allows for volumetric analysis so that a computer program can reconstruct a 3D image of the tissue sample.
But since the 200 nm gold particles are smaller than the resolution of x-ray tomographic microscopy, the researchers then used transmission electron microscopy to determine the precise location of these molecules. In order to do so, they chopped up their perfused tissue samples with serial sectioning. After correcting for rotation (which tissue samples are liable to do in the microtome), they found a high degree of correlation between their recounstructed image stacks and the real slices. They were also able to track the 200 nm gold particles over a series of TEM images, as shown via the arrow in these two slices 80 nm apart:
One might imagine neuro investigations using tomographic microscopy to build 3D models of a given tissue region and then confirming the precise location of individual structures (like synaptic ribbons) within the 3D space via electron microscopy.
Haberthur D, et al. 2009 Multimodal imaging for the detection of sub-micron particles in the gas-exchange region of the mammalian lung. Journal of Physics: Conference Series 186. doi:10.1088/1742-6596/186/1/012040. Link.