Serial Section Reconstruction Overview

Watch our webinar on Brain Mapping.

Preparation

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. Consult the recommended procedures below:

Serial Section Reconstruction

• Live images
  • One section per slide
  • All sections mounted on one slide
• Acquired images
  • One section per image
  • All sections on one image (delineation and alignment one section at a time)
  • All sections on one image (delineation of all serial sections before alignment)

3D neuronal Reconstruction

• Tracing neurons in serial sections

Tools

Stereo Investigator provides a variety of tools to perform serial section reconstruction:

 

Data visualization	Commands	Automated methods
Serial section manager Image organizer Macro View 3D visualization Where Is combined with Select Objects	Open files into serial sections Move image & tracing Match Align contours to center (CTRL-F) Select everything this color Edit individual points	Outline detected objects Mark detected objects Automatic contouring

 

---

Stereo Investigator 11 | MBF Bioscience Support Center | Downloads