Structures of interest were reconstructed and quantified from the serial EM images, with the 3D reconstruction software, Reconstruct (http://synapses.clm.utexas.edu/tools/index.stm) (Fiala, 2005).
The P3DS consists of an LED light source, diffuse screen, step motor, CCD camera, and scanner management software with 3D reconstructed software.
Sections were photographed using EM, and aligned into a 3D volume using Reconstruct software.
Three-dimensional smoothed surface images were made using the Reconstruct software (version 1.1.0.0 - John C. Fiala, Austin, Texas, USA) [42].
To facilitate the tracing of complex bundles of axons we enhanced the Reconstruct software [6], which was initially developed for manual segmentation of serial section electron microscopy.
A region growing algorithm was implemented in the open-source Reconstruct software and applied to the semi-automatic tracing of individual axons in three dimensions.
Although the Reconstruct software can montage multiple images in each section, the fact that different stacks were re-sampled in different directions made it necessary to use Reconstruct to trace one stack at a time.
Using the Reconstruct software (Synapse Web, Austin, TX), receptive field boundaries were drawn over images of the hand and digits, and receptive field sizes were calculated by the software.
All reconstructed pyramidal cell somata were exported with Reconstruct software as a vrml file.
Reconstruct software was then used to align the tissue slices and automate AuNR recognition.
