MultiTracer

MultiTracer is a Java application for displaying three-dimensional images and defining anatomic structures within these images. The tracings of structures can be saved in a format that facilitates review and revision, and the volumes, areas and lengths of traced structures can be computed. The traced structures can also be exported in the UCF format that is used by many of the tools in the UCLA Laboratory of Neuroimaging. These include tools for simple measurements (e.g., areas, volumes, lengths, width, surface areas, etc.) as well as tools that resample the tracings into surface meshes that can be analyzed and displayed.

Current Version

MultiTracer version 2 is now available. This page provides legacy documentation for MultiTracer version 1

The final release version of MultiTracer version 1 was May 22, 2005. You can verify that you have the latest release by checking the "About" menu item under the "File" menu.

Revision history

Requirements

• Java 1.4 or higher (available for PC's, Mac OS X, and most UNIX platforms)
• Images must be 8- or 16-bit grayscale images in one of the following formats:
  • Analyze Image format (PC or UNIX)
  • Medical Image NetCDF (MINC) format
  • uncompressed Tagged Image File Format (TIFF)
  • zipped TIFF format
  • Graphics Interchange Format (GIF)
  • Joint Photographic Experts Group (JPEG) format
  • Bitmap format (BMP)
  • Flexible Images Transport System (FITS) format
  • Raw format (user supplies relevant information)
  • Other file formats can be supported by writing custom Java code

Topics

Descriptions of the following topics are available:

• Downloading MultiTracer
• Launching MultiTracer
• Loading or importing
  • the first image
    • loading
    • importing
    • importing using a URL
    • importing raw data or using custom Java code
  • additional images
    • loading
    • importing
    • importing using a URL
    • importing raw data or using custom Java code
• Adjusting image brightness
• Changing image orientation
• Handling anisotropic voxels
• Changing image display size
• Choosing the image interpolation method
• Viewing data
• Refreshing the display
• Changing the volume displayed in orthogonal windows
• Using the cursor to identify homologous points in different volumes
• Creating or displaying annotations
• Defining a structure that will be traced
• Setting the color used to display a structure
• Tracing a defined structure
• Quick and Dirty threshold based tracing using the Wand
• Modifying a traced contour
• Saving contours
• Reloading saved contours
• Exporting contours as UCF's
• Calculating structure volumes
• Calculating structure areas and lengths on a given plane
• Analyzing UCF's
• Computing the MINC world coordinates of contours
• Documenting anatomic protocols
• Unloading additional images
• Editing an image
• Saving an image
• Repairing a badly edited image
• Quitting MultiTracer
• Acknowledgments

Modified: May 22, 2005