STERECON is a facility for making contour-based 3-D reconstructions from microscope images.
Useful for:
It is distinguished from other contour-based 3-D reconstruction programs in that contours can be drawn in 3-D while viewing micrographs stereoscopically. Stereoscopic tracing within a 3-D image is very helpful when branching or multiple structures are being studied. Correct continuity of structures is immediately recognized in a single 3-D image, without the need to refer backwards and forwards in a series of 2-D serial sections. In addition, low-contrast structures become more apparent and better-defined when looking through a volume rather than at individual slices.
For EM, multiple levels can be contoured in thick sections from the HVEM or IVEM, avoiding the inconveniences of using large numbers of thin sections, but without the loss of z-resolution normally associated with the use of fewer sections. Conversely, serial thin sections can be combined into artificial thick sections which can be traced to better advantage stereoscopically. The same technique can be used for LM histological sections. For electron tomographic or confocal LM z-series volumes, tracing can take place in the entire volume or in a series of overlapping thick sections.
After tracing, contours are combined and displayed as reconstructed objects. Examination of the reconstructions using various orientation and presentation choices (stereo, color, rotation, surface rendering, etc.) can lead to fresh insights into the structure, function and interaction of organelles. The contour data also provides the 3D coordinates needed to calculate absolute volumes, surface areas, perimeters, etc. Such quantitation is independent of cell anisotropy and so avoids the sampling errors inherent in stereology of single random sections. Images not already in digital form are scanned using a rapid, high-resolution (up to 2048x2048 pixels) TV digitization system consisting of a modified Dage model 81 camera with an Androx ICS-400 image capture and processing board in a Sun workstation. Serial section and stereopair alignment is done at the scanning step using real- time overlayed images or a fiducial grid. Alignment can be further refined when the images are displayed for tracing. Zoom and pan functions are available during the tracing process to enable fine details, as well as large-scale structures to be traced in the same image. Tracing is done manually using a 3-D cursor, either on parallel planes (for space-filling objects) or as free 3-D lines (for filamentous objects). Contours can also be traced automatically if the structures of interest are well contrasted from their surroundings (as is often the case with confocal LM when specific stains are used).
There are two STERECON workstations at the BMIRR. One uses an two-monitor stereo graphics terminal on a Sun host. The newer workstation second uses a Silicon Graphics Indigo2 workstation equipped for stereoscopic viewing, and digitizing tablet for contour input.
The system was developed at the BMIRR by A. Leith and M. Marko, and has
been in use since 1985, with continuous upgrading.
A summary of some other free and commercial serial section reconstruction
software is also available here.
Some reconstructions done with STERECON:
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