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Serial Section Reconstruction from Images (Procedure 1)

Use these instructions if you have one section per image. Scaling should be identical for all the images.

If contours are already traced in each image, consult this alternate procedure.

1. Open the Macro View () and the Image Organizer ().
2. Open the Serial Section Manager (Tools>Serial Section Manager).
   1.  Select Show Current Section Only and Show Suppressed as Gray
   2. 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.
   3. Highlight the first section.
3. File> Image Open to load the first section to be traced.
4. 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>Automatic Object Detection>Outline Detected Objects
5. Go to the next section to be traced:
   1. File> Image Open to load the next section to be traced.
   2. Make sure the contour you just traced is not grayed out. See details in Serial Section Manager: Buttons>Show Suppressed as Gray.
      • If it is grayed out: In the Serial Section Manager, select the section above the section currently selected (in other words, select the section in which you just traced the contour instead of the section containing the tissue to be traced) and verify that the contour is colored.
   3. Make sure the image of the new section is displayed in the Image Organizer.
6. Align the already traced contour and the image of the section to be traced.
   • 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. Exit the Edit mode.
   • Use the Tools>Match method.
7. In the Serial Section Manager, select the section number corresponding to the section to be traced.
   • The previously traced contour appears in gray.
8. Trace the contour using your preferred method.
9. Repeat steps 5 through 8 for the next sections to be traced.
10. 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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