Serial section reconstruction with image stack

Purpose

This approach will automatically create sections via the Serial Section Manager:

  • The Evaluation interval is set to 1
  • The Cut thickness is set to the z spacing of the stack

Use this approach when:

  • The image stack is based on either whole slide images (with a large distance between images in z) or EM (with a very small distance between images in z).
  • The image stack contains the entire structure to reconstruct.

Procedure

  1. Use File>Open>Image stack to open the image stack.
  2. Open the Serial Section Manager (Workspace>Tracing>Serial Section Manager) and the Image Organizer (Workspace>Image>Organizer).
  3. In the Image Organizer, right-click the stack name then select Create sections from this stack from the right-click menu.
  4. Use the Serial Section Manager to navigate through your image stack and trace the structures (see Tracing contours (2D)

  5. You can use the PageUp/PageDown keys or the mouse wheel button to navigate through your image stack but tracing is restricted to the section selected in the Serial Section Manager (i.e., current section).

  6. Visualize the reconstruction in 3D:
    1. Open the 3D Visualization window (Workspace>Views>3D visualize).
    2. Display the Contours panel, select contours then select Shell from the Show as drop-down menu to display the contours as a single volume. (If you only see one contour, return to the Serial Section Manager and click the Show current section button to turn it off. )
    3. Drag the mouse to rotate the reconstruction.
    4. Use the Imagepanel to adjust how your image stack is displayed.

    Click the Eye icon in the Image Organizer to show or hide your image in the 3D window.