About Anatomy Links Publications Search Tools

Synapse Web hosts a suite of tools for analysis and reconstruction
of three-dimensional objects from serial sections.

List of Current Tools:
Tool Platform Function
Reconstruct Software Win32* Colorize, montage, align, trace, measure and reconstruct serial section images.

Reconstruct was written by John C. Fiala, Ph.D.
For more info go to Reconstruct HistorySightings, and Reconstruct User Manual (4.2Mb).

Publication regarding Reconstruct:  Fiala JC (2005) Reconstruct: A free editor for serial section microscopy. J Microscopy.

List of Old Tools:
Tool Platform Function

sEM to Reconstruct file converter Win32*  To import an sEM Align series to a Reconstruct series
IGL to Reconstruct file converter Win32* To import an IGL Trace series of images and contours to a Reconstruct series
Trace Win32* Identify, measure, outline and reconstruct objects from serially-section images.
Align Win32* Align 8-bit grayscale serial section images.
Convert Win32* Convert a set of image files to 8-bit grayscale for use with IGL Trace or sEM Align.
MergeWRL Win32* Merge a set of reconstructed objects (.wrl files) into a single scene (.wrl file).
VRML Converters Win32* Convert between 3D file formats, e.g. VRML 1.0 to VRML 2.0.
VRML Viewers Windows View IGL Trace 3D output graphically using a VRML standalone viewer.
VRML Plugins Windows
w/Web browser
View VRML 1.0/2.0 objects from your web browser.
3D Editors/ Renderers Windows Import multiple VRML objects into a scene, change colors or lighting, and generate a high-quality rendered image.
EasyZIP Win32* Extract files from .zip archives into any directory.
Internet Tool Database Various A searchable database of HBP-related software tools for neuroscience.

* Win32 applications run on Intel versions of Windows XP, 2000, NT, 9x, and sometimes even Windows 3.1x when the Win32s libraries are installed.