About Anatomy Links Publications Search Tools

Trace is a Windows (Win32) application for identifying, tracing, measuring, and reconstructing objects in three dimensions from serial section images. IGL Trace is designed to operate on aligned sections obtained from sEM Align.

Download Version 1.26b (673K zip) [Last update: Apr 25, 2001]

Download Example Data (1.2M zip) [Last update: Jan 7, 1999]

Printable IGL Trace Help (101K pdf) [Last update: Apr 25, 2001]

Answers to Frequently Asked Questions about IGL Trace. [Last update: Jan 26, 2001]

System Requirements:

Microsoft Windows

2Mb of disk space for program files

16 Mb of RAM (or more depending on your OS and image size)

Enhancements in version 1.26b:

Enhancements in version 1.24b:

Input formats:

IGL Trace accepts data images in GIF, JPEG, TIFF, Windows BMP, and IGL formats. IGL Trace can be customized to handle additional formats by dynamic link library input filters. If used for reconstruction, the serial sections should be aligned prior to using IGL Trace.

Although designed especially for use with serial electron microscopy (EM), IGL Trace will also work with images obtained from confocal and light microscopy. IGL Trace can directly import Noran Intervision files and can import other image stack formats using a Generic format importer.

Here's an example reconstruction of a 30-micron pollen grain. It was imaged using Noran OZ confocal microscope. Z-spacing was selected to produce a section thickness of 0.75 microns, resulting in 46 sections to image the entire object. The gray-scale intensity images were imported into IGL Trace. The boundaries of the in-focus part of the object in each section were outlined using IGL Trace's automatic tracing feature, with a section-by-section manual adjustment of the intensity threshold to compensate for uneven bleaching during acquisition.

Exported formats:

IGL Trace can export contours of traced objects in a number of formats including Steve Young's HVEM format, universal contour file format, ROSS contour file format, AutoCAD DXF, and NUAGES contour format. For the pollen grain, contours were exported from IGL Trace in NUAGES contour format. The three-dimensional object was then reconstructed using the NUAGES package of Bernhard Geiger on an SGI Indy workstation.

IGL Trace can also generate and export 3D objects in VRML 1.0 format. These include individual points or contour centroids, contour lines, planar slabs, and fully-surfaced 3D objects. This image of a dendrite was reconstructed from serial EM by generating a surface in IGL Trace and then importing this VRML object into 3DStudio MAX on a Pentium II PC for final rendering.

In addition, IGL Trace can output measurements of traced objects including counts, 2D areas, centroids, 3D surface areas, and volumes.

Previous Versions:

Version 1.24b (497K zip) [Last update: Dec 27, 2000]

Version 1.01b (796K zip) [Last update: Jan 3, 2000]

Note that this version received a couple of years of testing and performed well despite a few bugs and unpleasant features. If there are majors problems with the latest version, try this one instead. This version is recommended for Windows 3.1 users. It has 8.3 file name restrictions. The last release of IGL Align is also included in the zip file.

Last Updated: 6/6/01