SliceApp

• Invocation
• SliceApp window
• Output window
• SliceApp Control Panel
• Image window

Invocation

java SliceApp [image file]

SliceApp window

• Image file
  Enter the name of the ANALYZE image in this textbox. You don't need the .img or .hdr extension. The file can be compressed or gzipped.
• Run
  Run will bring up the image display and its control panel.
• Cancel
  Cancel will kill the entire application.
• Help
  Help will start up netscape on whatever machine you are running the application on, with the html help document for SliceApp. All CCN lab java help documents are also available at a kraeplin java doc site.

Output window

SliceApp Control Panel

• Slice
  The slider lets you change slices.
• xyz
  The x y z text fields show the location where the last mouse click occurred (upper left of first slice = 0 0 0), and thus show the location for the intensity value displayed in the Value field. You can enter x y z coordinates in these fields and the Value field will update accordingly. You must hit return in EACH textfield that you change.
• Value
  The Value textfield shows the intensity value (disk value, not affected by Brighten/Darken buttons) of the voxel selected by the last mouse click or entered in the x y z fields.
• Mag.
  The Magnification choice widget lets you change the magnification of the image display. (If you try to magnify a 256 x 256 image you will probably run out of memory.)
• Brighten / Darken
  The original colormapping is a linear mapping of disk values to a grayscale in the range of 0-255. Use the Brighten / Darken buttons to adjust the grayscale mapping.
• Add Overlay
  The Add Overlay button will bring up a dialog box that lets you enter an image filename that will be used as an overlay on the existing image display. You need to enter the following information in the Overlay Dialog Box:
  • File
    Enter the name of the ANALYZE file to be used as an overlay image. It must be the same dimension as the image you are viewing.
  • Lower / Upper Threshold
    By default, all voxels in the overlay image whose intensity value is greater than zero will be included in the overlay. You can set an upper and lower threshold so that fewer voxels are included in the overlay.
  • Color
    Choose a color for the overlay. If pixels are included in more than one overlay, the color values are simply added, if too many colors are added the result will be white.
  • Add
    Clicking Add will update the image display with the selected overlay and close the dialog box.
  • Cancel
    Clicking Cancel will close the dialog box without updating the image display.
• Remove Overlay
  All overlays you have added are listed in the Remove Overlay choice widget. Select an overlay from this list to remove it from the image display.
• Add timeseries plotter
  Use this button to add an interactive graph display to plot timeseries data. Once you have a graph display, clicking on a pixel with the middle mouse button will add that pixel's timecourse plot to the graph. You must have appropriately formatted timeseries data to get the plots. The java Permute application formats data correctly. When you select the Add timeseries plotter button, a dialog box will pop up to get the timeseries information:
  • File
    Enter the name of the Pgh1.0 file that has the timeseries data. The java Permute application can create the necessary file.
  • Add
    Clicking Add will bring up the graph display and close the dialog box.
  • Cancel
    Clicking Cancel will close the dialog box without starting up a graph.
• Quit
  Quit closes the Control Panel and its associated image display, it does not close the SliceApp window.

Image window

• The image window displays a grayscale representation of the image file. java uses 1 byte per colorband to represent images, so disk values have been scaled such that max/min values map onto 255/0.
• Clicking on the image with the left mouse button updates the x y z and disk value information in the Control Panel.
• Clicking on the image with the middle mouse button updates any timeseries graphs that have been started.

• Menubar
• Toolbar
• Output window