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 Help › Update 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
To use the VisBio Ortho Stack plugin, you must first open an image stack. For example, you could use File › Import › Image 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 Plugins › VisBio › Ortho Stack
- To display every individual image within the view, unselect “Parallel projection”
- To compact the images, decrease the amount of stretch within the stack