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Serial Section Reconstruction: One Image with Multiple Sections (Procedure 1)

Use these instructions if you have one image file with multiple sections.

In this procedure, sections are delineated and aligned one section at a time. If you opt to delineate all your sections first instead, consult this alternate procedure.

1. File> Image Open this type of image→ .
2. Open Macro View and Image Organizer .
3. Open the Serial Section Manager (Tools>Serial Section Manager).
   1. Click the New Section icon to create as many sections as needed for the reconstruction.
      • The number of sections created corresponds to the number of sections to be traced.
   2. Highlight the first section.
4. In Macro View:
   1. Right-click over the image and select Go To.
   2. Click on the section to be traced.
5. Zoom to a level suitable for tracing the region(s) of interest.
6. In the Tracing window, trace the region(s) of interest on the section using one of the methods below. You may want to trace fiducial contours.
   • Manually
   • Automatic Contouring
7. Go to the next section to be traced:
   1. Move>Move image.
   2. The cursor turns into a hand; drag to the section to be traced until the current contour(s) are approximately aligned with the section to be traced.
   3. Right-click and select End move image.
8. Refine the alignment between the already traced contour(s) and the image of the section to be traced.
   • Use the Tools>Match method or
   • Use the Select object method:
     1. Edit>Select All Objects
     2. In the Edit Tool panel, select Only Contours from the Select Objects drop-down menu.
     3. Right-click and select Move selected contour or Rotate selected contour.
     4. Align the contours.
     5. Close the Edit Tool panel to exit the editing mode.
9. In the Serial Section Manager:
   1. Select Show Current Section Only and Show Suppressed as Gray .
   2. Select the section number corresponding to the section to be traced.
      • The previously traced contour appears in gray.
10. Trace the region(s) of interest using your preferred method.
11. Repeat steps 7 through 10 for the next sections to be traced.
12. Visualize the reconstruction in 3D.

    Only images that are not in virtual image mode can be displayed with 3D Visualization.

    1. In the Serial Section Manager, click Display Current Section Only to disable it; you should see all the contours in the chosen contour color.
    2. Click the 3D Visualization icon .
    3. Select Surface Reconstruction from the Contours options.
    4. Rotate the reconstruction.

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