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Reconstruct - History

The origins of Recontruct began in 1995 with the development of a Windows 3.1 program for tracing serial sections. WinV8 was developed in the Image Graphics Laboratory at Children's Hospital, Boston, as a continuation of the DOS-based V8 program developed by John Davis.

Very quickly WinV8 was replaced by a new Win32 application, IGL Trace. Version 1.0a of IGL Trace was completed in August of 1997, with NIH funding (J. Volpe, PI). IGL Trace has proven useful for identifying, tracing, measuring, and reconstructing 3D objects in serial sections in a number of scientific studies. For examples see usage page.

IGL Trace was designed to operate on aligned sections. These can be images obtained from electron or light microscopy. In the case of confocal images, a z-stack is usually already well-aligned. Here's an example reconstruction of a 30-micron pollen grain 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.

For electron microscopy, where each section is imaged separately, it is necessary to realign the images for accurate reconstructions. IGL Align, also developed in the Image Graphics Laboratory, was a first attempt at aligning grayscale images. Funding from NIH's Human Brain Project to Children's Hospital allowed the development of a more sophisticated alignment program, sEM Align, in 1999. sEM Align was developed to allow on-screen alignment of larger images than was possible through the use of IGL Align. This is accomplished by displaying and moving scaled versions of the original images on screen. Images can be incrementally moved using keyboard input or alignments can be computed from a set of feature correspondences specified by the user. To use the alignments computed by sEM Align, a new set of aligned images are rendered for input into IGL Trace.

Most of the functionality of sEM Align and IGL Trace is incorporated into Reconstruct. Reconstruct was developed with continued funding from NIH's Human Brain Project (K. Harris, PI). By combining alignment and tracing into one program, Reconstruct allows images to be processed more efficiently. Tracing can be done directly on the transformed images and alignments can be easily modified. To convert an existing sEM Align series to one compatible with Reconstruct use the sEM to Reconstruct file converter. To convert an existing IGL Trace series to one compatible with Reconstruct use the IGL to Reconstruct file converter.

Reconstruct offers a number of advantages over IGL Trace and sEM Align, including:

  • montaging within a section
  • alignment of color images
  • storage of alignment traces
  • section browsing as thumbnails or flipbooks
  • fixed aspect ratio of displayed sections
  • improved drawing tools with automatic elimination of loops
  • color-filled traces
  • stereological grids and sampling frames
  • object (all traces) editing
  • longer trace names with automatic trace numbering
  • scaling and nonlinear transformation of traces
  • multiple selection editing
  • comprehensive undo operations
  • more 3D object generation options
  • interactive 3D scene composition, coloring, and transparency
  • VRML 1.0, 2.0, and bitmap image output

To access the old synapses.bu.edu tools follow these links: