Multiple sections per image (option 2)

Serial section reconstruction procedure

 

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

 

1. File>Open>Image opens this type of image→ .
2. Open Macro View and Organizer.
3. Delineate the sections using your preferred method:
   • Trace>Automatic>Outline objects
   • Manually
   • Automatic contouring
4. Optional: Mark cells of interest using Trace>Automatic>Mark objects.
5. Open the Serial Section Manager.

   Click the New Section icon to create as many sections as needed for the reconstruction.

6. Assign each contour to a serial section (you need to know in which order your sections have been mounted).
   1. Use Trace>View>Where Is and Trace>Edit>Select objects to see the contours only.
   2. Click a contour.
   3. Right-click and select Place Contour in Section. The Select Section window opens.
   4. Select the appropriate section.
   5. Repeat Steps b-d for each successive section.
7. Turn off the Where Is and Edit modes by clicking their icons again.
8. Press CTRL-F to align all the sections.

   Alignment is performed based on the midpoint of each individual contour.

9. Press CTRL-F again to return to the display of contours over the different sections.
10. Visualize the reconstruction in 3D provided that the sections are sufficiently apart in z.

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

    1. Open the 3D Visualization window (Workspace>Views>3D visualize).
    2. In the Contours panel, select Shell from the Show as drop-down menu.
    3. Rotate the reconstruction.