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VisBio Ortho Stack

The VisBio Ortho Stack plugin is a simple 3D visualization plugin for Fiji that displays a stack of image planes in a parallel or perspective projection along the z plane. The plugin can control several common operations, such as specifying distance between cross sections, rotating and zooming the RD view, and saving a snapshot of the current image to a file.

Updating the VisBio Plugin

The VisBio Plugin is part of the LOCI update site:

  • Select HelpUpdate Fiji
  • Once the ImageJ Updater is presented, select “Manage Update sites”
  • Select the “/orgs/loci” site to update all LOCI plugins, including VisBio
  • Close “Manage Update Sites” and select “Apply changes”
  • Restart ImageJ and the update will be in effect

Using VisBio

To use the VisBio Ortho Stack plugin, you must first open an image stack. For example, you could use FileImportImage Sequence and select the folder of images you wish to use.

After you have your image stack imported, follow the following directions:

  • Select the imported image sequence
  • Select PluginsVisBioOrtho Stack
  • To display every individual image within the view, unselect “Parallel projection”
  • To compact the images, decrease the amount of stretch within the stack

The first image within the Ortho Stack


Last image in the Ortho Stack


A cross sectional view of the Ortho Stack