Serial Section Reconstruction Overview

Watch our webinar on Brain Mapping.

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 differ depending on the type of reconstruction and the medium. Consult the recommended procedures below:

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)

Microlucida 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