Tools: Volume Integration and Alignment System (VIAS)

Version 2.4, last updated on January 26, 2009.

System Requirements:
  • Windows 98/NT/2000/XP
Online help manual.

VIAS stands for Volume Integration and Alignment System. It is designed to allow multiple stacks of tiled optical sections obtained from Laser Scanning Microscopy to be integrated into a single volumetric dataset. Currently only 8 and 16 bit grayscale images are supported.

VIAS has been designed with large datasets in mind, for which volume integration is a prerequisite if the dataset is to be used for extraction of cell structure and visualization.

VIAS allows the user to select the individual image stacks from disk and to adjust their relative position on the screen interactively. VIAS makes use of projected volumes and hardware accelerated drawing to provide real-time interaction with the data. An auto align feature corrects any small mis-alignments in the manual placement of adjacent images. This ensures that the tiling is accurately reassembled before the volume is integrated. The user can manipulate the stacks using a global 3D coordinate system and execute the integration of the data after all the stacks of images have been correctly positioned.


  • Batch open multiple stacks
  • Support for .raw, .tif and Bio-Rad(.pic) images
  • Support for 3D files
  • Stack locking
  • Customizable workspace display
  • Pixel sampler tool
  • Alignment reference grid


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