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Flipping a single section with a completed tracing

Serial Section Reconstruction Overview

 

You have completed tracing a data file and notice that one of the sections appears to be upside down.

Flip the problematic section:

  1. Select the section to flip. ClosedHow?
    1. In the Serial Section Manager, click the icons Show Current Section Only and Show Suppressed as Gray;
    2. Select the section to flip; the selected section appears in color, while all other sections appear with gray lines.
  2. Optional : If Z positioning is critical, determine the z position of your deepest traced point or the bottom of the tissue section for the section to be flipped with Orthogonal View.
  3. Flip vertically (or horizontally). Closed How?
    1. Click Edit>Select All Objects.
    2. Right-click in the Tracing window and select Flip Selected Objects from the menu . The Flip Selected dialog box opens .
    3. Select Horizontal and/or Vertical flip.
  4. Optional : If Z positioning is critical, correct the depth values of the flipped data to match them up with the original sections. ClosedHow?
    1. Select Tools>Shrinkage Correction. Enter "-1" as the factor .
    2. Calculate the correct delta.
    3. Right-click and select Modify Z Position. Select Shift Z values and enter the delta value calculated in step 4.b.
  5. Align the section with those above and below it. ClosedHow?
    1. Click Edit>Select All Objects.
    2. Right-click and select Move Selected Objects or Rotate Selected Objects.

Use Move>Where Is to see the entire tracing while you reposition the section.

 

Example

  1. Select Section 2 to flip.
  2. Deepest traced point: Z=600.00 (see illustration above).
  3. Flip vertically.
  4. Correct the depth values of the flipped data to match them up with the original sections.
    1. Shrinkage correction: -1. The deepest Z value is now -600.00 and all other points have a negative z value.
    2. Correct delta: The deepest traced point located at -600.00 should actually be located at 500.00 (the top of the section). This means that we need to shift the Z values in this section by 1100:

    1100=500.00-(-600.00)

    1. Right-click and select Modify Z Position. Select Shift Z values and enter 1100.
    2. Verify that the deepest traced point Z value is now 500.00.
  5. Align the section with those above and below it.

 

 

Correcting for an upside-down section while tracing if you encounter an upside-down section while tracing neurons or contours.

 

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