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Scanner Basics

This section describes the way Scanner typically would be used for segmenting images. The usual process would be as follows:

  1. Load an image to segment. Click on the "Load Image" menu entry. This gives you a file browser that lets you move around in the UNIX file system. (To move to the parent of the current directory, click on "..") When you find the correct image, click on its name to load it. Clicking on "Exit" before you select an image will cancel the image loading operation and return you to the main Scanner menu.
  2. Load a shape model. To use take advantage of Scanner's segmentation tools, you need to specify a shape model which corresponds to the organ you are trying to outline. Click on the "Load Model" menu entry. Again, this gives you a UNIX file browser. Locate the appropriate shape model and click on its name to load it. Once you return to the main Scanner menu, the "Model Status" menu (third from the top) will display information about the current model.
  3. Outline a shape. Once the correct image and shape model have been loaded, you can begin the segmentation process. Click on the "New Contour" menu entry. Then enter the two endpoints for the long axis of the shape. (The long axis is used to determine the position, scale, and orientation of the shape model.) When both points have been entered, Scanner will attempt to locate the shape's boundary along each of the radials in the contour. When the automatic segmentation process has finished, the main Scanner menu will return.
  4. Make corrections. At this point, you may make corrections to the contour. Changes to a radial can be made by placing the mouse at the correct location along a radial and clicking. You can also grab the end of a radial and drag it to the correct location. Most of the time, you will want to make corrections without interference from the shape model. To temporarily disable the model, click on the "Segmentation Options" menu entry. Set both "Use model?" and "Use edge detector?" to NO and click on "Exit" to return to the Scanner menu. (Note that you can leave the model active while you make corrections. For some shapes, this may even reduce the number of corrections you need to make. You may want to experiment with both approaches and see which works best for you.)
  5. Save the new outline. Once you have made any necessary corrections to the segmented contour, you need to save it. Click on the "Save Contour" menu entry. This brings up another UNIX file browser. Move to the directory where you would like to save the contour, type a name for the file, and press RETURN. (A more structured way of saving contours is on the to-do list.)

This basic segmentation process can be repeated for each image and shape that needs to be outlined. If you disable the shape model while making corrections, be sure to re-enable it before creating your next contour.

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