 Physical section thickness

Physical section thickness is the distance through a recovered physical section, measured normal to its faces. For a flat section with parallel faces, write this distance as $t$; a nonuniform section instead requires a local thickness or a stated averaging convention. It is distinct from the nominal section feed commanded to the microtome, the spacing of sampled planes in an image stack, and the spatial resolution of the resulting image.

In ultramicrotomy, a controlled advance presents material to a diamond knife on each cutting stroke. JEOL describes preset feed increments for thin sections and notes that actual thickness depends on the material and temperature.^[ref] Section compression and other deformation can further complicate the relation between the machine setting and the recovered section. A feed setting alone is not an independent thickness measurement.

An original geometric example shows why finite thickness matters. Consider a straight thin feature whose direction makes angle $\theta$ with the section's normal vector. Choose coordinates so the section occupies $0\le z\le t$ and the feature lies alongAn image combining contributions through the section can therefore contain feature positions spanning the lateral distanceFor stipulated $t=100\mathrm{nm}$ and $\theta =30^{\circ }$, this range is $57.7\mathrm{nm}$. It is a geometric range, not a universal formula for the measured image width: image contrast, the imaging response and the feature's own width also matter. Replacing the slab by one mathematical plane discards this depth variation.

For an ideal undeformed series of contiguous $100\mathrm{nm}$ sections, imaging every fifth section gives a centre-to-centre sampling interval of $500\mathrm{nm}$, while each imaged section remains $100\mathrm{nm}$ thick. Record omitted sections and the image stack axis calibration separately. To test a feed setting experimentally, measure recovered thickness with an independent method and stated measurement uncertainty, rather than using the same feed display as both command and verification.