Continuity Imaging Module

Note: the imaging module only works in Windows at the moment, although it should work from Linux and MacOS X in the future.

Generating Fiber angles

  • During start up, make sure the imaging module is checked on the splash screen. If you’re already running Continuity, load imagingCommands.

  • Click Imaging→Edit Images
  • Open an image (Select “File→Open…” from the menu in the “Edit Images” window)
    • If you don’t have an image, you can use this one

  • Repeat the previous step until you’ve opened all the images you want to analyse. You can also analyse images separately if you prefer.
  • To generate fiber angles:
    • Select “Segment→Fibers→Calculate Angles” from the menu. This may take a long time if you have a slow computer and/or you’ve loaded a large image.
  • To adjust the visualization properties of the fiber angles, select “Properties→fibers” from the menu. You might want to change the “width” to 2 or more.
  • To delete fiber angles, click the delete button (towards the left of the window) and then click on the fiber angle you wish to delete.
  • To export these resulting fiber angles (to a tab delimited file), select “Segment→Fibers→Export Angles.” When the table manager appears, select “File→Save” in the table manager’s menu.
  • To view statistics Segment→Fibers→Calculate statistics. If this generates an error, you may wish to decrease your x interval, y interval size.
  • You can also apply various filters and image enhancements (see the “Enhance” menu). These Enhancements are not applied to fiber segmentation or statistics unless you first select “flatten image” in the Layers menu.