Serial section reconstruction overview

Preparation

See also Preparing tissue

Determine the appropriate level of mapping accuracy:

  • If you need to map the precise location of objects within a section during a reconstruction, then it is important to mark the cells at the proper Z depth.
  • If you need to generate a map for visualization purposes, mapping the precise locations within a section may not be important; save time by mapping all objects at the same Z depth as used to trace the contour.

Procedures

Procedures differ depending on the type of reconstruction and the medium. Recommended procedures are listed below:

Useful tools

Data visualization

Commands

Automated methods

Troubleshooting: My reconstruction is not "skinning" properly in 3D

In the 3D visualization window, it is possible to connect one traced contour through the z axis to the next traced contour by "skinning" your reconstructed volume:

  1. Click the Contours button.
  2. Select contours (at least 3 contours are required).
  3. Select Shell from the Show as drop-down menu.

Sometimes, especially in more complicated reconstructions, the skin can’t be generated or does not look as it should. Here are a few things to try to solve this problem: