### Model Header Dialog

This dialog allows you to set several items in the model header.
The most complicated item is the Z-scale, which is used both to adjust
the model display to its proper dimensions in Z, and to account for
the Z dimension properly when extracting quantitative information.
For serial sections, the Z-scale is the ratio of section
thickness to pixel size. For tomograms, the Z-scale needed to account
for thinning is the ratio of
the original section thickness (typically the nominal thickness at
which the section was cut) to the thickness
of material in the reconstruction. If a shrinkage in X/Y is known or
can be estimated, then the Z-scale in each case would be the ratio
just described, multiplied by the shrinkage factor (e.g., 0.9 for 10%
shrinkage).
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

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. Points will be added at the given interval for image
zooms 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.

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