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Serial Section Reconstruction from one Glass Slide with Multiple Sections

1. Load the slide on the stage.
2. 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.
3. Select Move>Joy Free and navigate to the section to be traced using the joystick.
4. Right-click and select End Joy Free.
5. In the Tracing window, trace the contour of the section using one of the methods below. You may want to trace fiducial contours.
   • Manually
   • Tools>Automatic Contouring
   • Image>Automated Object Detection>Outline Detected Objects
6. Go to the next section to be traced:
   1. Move>Joy Free.
   2. Use the joystick to navigate to the section to be traced until the already traced contour is approximately aligned with the section to be traced.
   3. Right-click and select End Joy free.
7. Refine the alignment between the already traced contour and the tissue section to be traced.
   • Use the Tools>Match method or
   • Use the Select object method:
     1. Edit>Select All Objects
     2. Select the contours.
     3. Right-click and select Move selected contour or Rotate selected contour.
8. 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.
9. Trace the contour using your preferred method.
10. Repeat steps 6 through 9 for the next sections to be traced.
11. Visualize the reconstruction in 3D.
    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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