Correct Z shrinkage

Purpose

Use to change the scaling factor for the Z axis, for example to correct for shrinkage.

Background

Section shrinkage is likely to be different along the X, Y and Z axes, particularly along the Z (depth) axis. The standard model for shrinkage assumes that shrinkage is linear. This means that the shrinkage at the top of a section is the same as the shrinkage at the bottom of a section. In fact, it implies that the shrinkage occurs equally all along any axis of the tissue.

Shrinkage correction is easy to apply when shrinkage is linear. The Z axis is multiplied by a factor to adjust the data for shrinkage. Data entered after applying shrinkage correction is not affected.

This functionality is not available for spines, puncta, or varicosities detected in the 3D environment. Contact our support team for specific guidance on correcting shrinkage.

To adjust the scaling of the X or Y axis, see Adjust Scaling.

Example
A section cut at 80 µm shrinks to a thickness of 50 µm; 5/8 the thickness of the section when it was cut from the specimen. The correction factor is therefore 8/5 or 1.6.

  • Enter a Z shrinkage correction of 1.6 (8/5)

  • 50 µm X 1.6 = 80 µm (original thickness of the section)

Procedure

  1. Click Correct Z shrinkage in the Tools dropdown menu on the Trace ribbon.

  2. In the Shrinkage Correction window, type a value for the Z axis or use the arrow buttons to make adjustments.

    • Z axis: Type a value for the Z axis or use the arrow buttons to make adjustments.

    • Dynamically Update: Check the box to see changes as you make them.

    • Also Adjust Images: Check the box to apply your settings to the image file(s).

  3. Click OK to apply the changes or click Undo to return to the original values.

To apply shrinkage to a single section, click Show current section in the Serial section manager window before applying shrinkage correction.

It is important to determine how much shrinkage each section, or series of sections, has undergone during preparation.

Also see Correcting for an upside-down section while tracing, Flipping a single section with a completed tracing