Serial tomograms often have material missing between the ending slice of one and the starting slice of the next. This fact indicates that for many tomograms, the thickness of the remaining material underestimates the actual thickness by the amount of missing material. It is possible to compute a Z-scale that compensates for this as well. Thus, the complete formula with all these factors is:

Z-scale = S * O / (Mn + (T * P)) Or: Z-scale = S * O / ((Mp + T) * P) Where: S = Shrinkage factor (a number less than or equal to 1) O = Original thickness in nm P = Pixel size in nm T = Thickness of material in pixels Mn = Missing material, in nm Mp = Missing material, in pixels

If you do have an estimate of shrinkage and want more accurate estimates of sizes in the original material, an additional step would be to adjust the pixel size upward by 1/S. If you do that, measure and compute the Z scale from the above formulas first with the original pixel size.

The **Total Z-scale** text box allows you to enter a scaling factor for the
actual size of the pixels in Z (section thickness) relative to their size in
X and Y. This factor is equal to the Z-scale just described, provided the
tomogram has not been squeezed.

The situation is more complicated when a tomogram has been squeezed
more in Z than in X and Y. In this case, the Z-scale needs to account
for both this differential squeezing and the section thinning. The
line **Z/X pixel size ratio** will show the amount of scaling
needed because of the differential squeezing. If you select
**Set incremental Z-scale** then the **Added Z-scale** text box
will be enabled instead of the **Total Z-scale** text box, and you
can enter just the scaling needed to account for thinning (the factor computed
as described above.)

The **Draw model** checkbox toggles model drawing, just as the **T**
hot key does.

The **Resolution** text box determines the spacing between successive
points when adding points continuously while holding down the second
mouse button. The behavior depends on the image zoom divided by the screen
scaling factor for a high-DPI monitor. Points will be added at the given
interval for this scaled zoom between 0.75 and 1.5), and at proportionally
bigger or smaller intervals for zooms lower or higher than these values,
respectively.

The **Pixel size** text box allows you to set the pixel size of
the model, which is needed for extracting quantitative information.
Enter a number then the units of measurement. Available units are
km, m, cm, um, nm, A, and pm. When a new model is created in 3dmod,
this pixel size will be initialized from the pixel spacing in the
image file header if the spacing is different from 1.