= Serial-section electron microscopy
<Serial-section electron microscopy> reconstructs a <volume> from an ordered <image stack> of thin physical slices. In the <transmission electron microscopy> implementation, an <ultramicrotome> cuts successive slices, which are collected on a support and imaged through the specimen. <Image registration> aligns corresponding features; <image segmentation> identifies structures to follow between slices. JEOL's glossary describes sections of 40–100 nm and illustrates the separate registration and segmentation stages.<Serial Section TEM by JEOL>[Definition and Figure1(a)–(e)]{ref}
The motivation is geometrical: one isolated slice cannot show whether a feature continues, divides, or ends outside that slice. An ordered <image stack> provides observations along the third coordinate, although finite <section-thickness anisotropy> and missing material limit what can be inferred. A change between neighboring images may come from specimen structure, a slice deformation, or imperfect <image registration>.
For a chosen numerical example, suppose each of $N=200$ consecutive sections has uniform thickness $\Delta z=50\,\mathrm{nm}$, with lateral <pixel pitch> $p=4\,\mathrm{nm}$. Ignoring lost material and thickness variation, the sections cover
$$
L=N\Delta z=10\,\mu\mathrm m,\qquad
V_{\mathrm{voxel}}=p^2\Delta z=800\,\mathrm{nm}^3,\qquad
\boxed{\frac{\Delta z}{p}=12.5.}
$$
The <voxel> sampling is 12.5 times coarser along the cutting direction. These are chosen dimensions, not measurements from either cited experiment. The first and last section centers are only $(N-1)\Delta z$ apart: center-to-center extent differs from total represented thickness. Neither spacing is automatically the achieved <spatial resolution>.
<Image resampling> onto a cubic grid can make an <image stack> easier to display, but <interpolation> supplies no additional independent observations. Likewise, smooth <image registration> cannot resolve <missing-section ambiguity in volume reconstruction>: a small connecting feature could lie wholly inside lost material. Checking a reconstructed connection therefore needs evidence in the acquired slices, not just a visually smooth rendered surface.
A historically important automation change illustrates the distinction between section and surface imaging. In 2004, <Winfried Denk> and <Heinz Horstmann> placed an <ultramicrotome> with a <diamond> knife inside a <scanning electron microscope>. Their <serial block-face scanning electron microscopy> imaged the exposed block surface between cuts instead of collecting the removed sections. They reported stacks several hundred layers deep, 50–70 nm sectioning, and typically less than 10 nm <lateral position jitter>. These observations tested an apparatus for acquiring closely aligned serial images; they did not remove the finite spacing between observations.<Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure by Winfried Denk and Heinz Horstmann>[Abstract; Results, lateral-position stability; Materials and Methods, Microtome]{ref}
A mechanical detail makes the measurement chain concrete. Their specimen-advance <lever> reduced the <motorized micrometer>'s motion by 0.11. Thus its stated position <measurement uncertainty> of 50 nm contributed $0.11\times50=5.5\,\mathrm{nm}$ after that reduction; other sources of section-thickness error still required assessment.<Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure by Winfried Denk and Heinz Horstmann>[Materials and Methods, Microtome, specimen-advance mechanism]{ref}
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