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))
    Z-scale = S * O / ((Mp + T) * P)
    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.

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