Shrinkage correction

Context

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.

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)

Applying shrinkage correction

  1. Click Trace > Tools dropdown > Correct Z shrinkage.
  2. In the Shrinkage Correction dialog box, type a value for the Z axis or use the arrow buttons to make adjustments.
    • To see your changes as you make them, check Dynamically Update.
    • Also Adjust Images applies the factor to images.
  3. Click OK to apply the changes or click Restore to return to the original values.

To apply shrinkage to a single section, click Show current section in the Serial Section Manager window.

To apply shrinkage to all of the data in the file, click Show current section again to disable it.

 

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