User manual SCION IMAGE FOR WINDOWS

[. . . ] Scion Image for Windows Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 System Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Menus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 File Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Options Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Process Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Analyze Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 Special Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Stacks Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Windows Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 T o o l s . 62 Image Windows. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 Map Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Histogram Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 LUT Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Paste Control Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Plot Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 Info Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Techniques . [. . . ] Since the projection routine assumes volumes contain one or more objects within a black background, use "Invert" to invert volumes with a white background. For low contrast volumes, increase the contrast using the controls in the Map window and then apply the look-up table to the volume using the "Apply LUT" macro. The "Remove 0 and 255" macro changes pixel values of 0 and 255 to 1 and 254 respectively. Use "Replicate Slices" to eliminate the gaps seen in projections of volumes with a slice interval greater than one by increasing the number of slices. The "Make Cone" macro creates a 643 volume containing a cone with two rods inside that is very useful for understanding the effect of various projection parameters. Reslice Reconstructs a 2D image from the image volume contained in the current stack. Use the straight line selection tool to select were the reconstruction will be done. You will be prompted for the slice spacing (displacement between slices in the stack) in pixels if this information has not been previously entered. Macros are available (in the file "Stacks") for repetitive reslicing of image volumes, for example, to generate a set of coronal slices from an MRI volume consisting of sagital slices. Stack Info. . . Allows you to view and set the type, slice spacing, and frame interval of the current stack. 54 A Volume is a stack containing a 3D Image. A Movie is a sequence of frames captured using the Make Movie Command. An RGB Image is a 3-slice stack containing a 24-bit color image in RGB (Red, Green, Blue) format. An HSV Image is a 3 slice stack containing a 24-bit color image in HSV (Hue, Saturation, Value) format. Interval is the inter-frame interval in a movie. RGB to 24-bit Color Converts an RGB color image (in the form of a three slice stack) to a 24-bit color image. Filter operations such as smoothing and sharpening cannot be performed on the 24-bit image they must be performed on the RGB slices. 24-bit to RGB Color Converts a 24-bit color image to an RGB three slice (red, green, blue) stack, a format that allows filter operations such as smoothing and sharpening to be performed. A macro can be created to automate the filtering process. 55 Windows Menu Next Window Deactivates the current image window and activates the next image in the image list, as shown at the bottom of the Windows Menu. Cascade Windows Expands all the image windows to their original size and redraws them slightly offset from each other. If you hold down the Shift key, all windows will be drawn in the same location, at the upper left corner of the screen, next to the tool palette. Tile Windows Shrinks all the images windows and repositions them so that they will fit on the screen without overlapping. Hold down the Shift key to draw tiled windows in "Scal To Fit" mode Scion Image supports "synchronized scrolling" of tiled windows. To try this out, open two or more windows (they must be the same size), tile them using Tile Windows, zoom in on one of them, then pan one of the images with the Scroll Lock key down. Notice how all the other images zoom and pan to the same relative location. Show Paste Control This will bring up the Paste Control dialog box. See Paste Control in the Windows section. Show Full Path Names If this item has a check next to it then the full path of files (text or images) will be shown on the title bar. 56 TOOLS The window containing the tool palette, as well as all other windows displayed by Scion Image can be freely moved around the screen. All the tools work with images at any of the eight available levels of magnification. One of the tools (the line selection tool) has three variations selected using a pop-up menu. Magnifying Glass Click within the active image window to zoom. Double-click on the magnifying glass icon to revert to 1:1 magnification. [. . . ] TileWindows Repositions and resizes all open image windows so they don't overlap. UndoBufferSize Returns the current size of the Undo and Clipboard buffers. UpdateResults Redisplays last measurement in Info and Results windows. VideoMath(`op', picnum, gain, offset) Where `op' is one of `add', `sub', `mul', `div', `and', `or', `xor', `max', and `min'. [. . . ]