IDL Slicer The IDL Slicer displays slices and isosurfaces created from three-dimensional volume cubes. Using the IDL Slicer Before calling the Slicer, you must define the common block VOLUME_DATA to include a variable that contains your 3D image dataset. The Slicer reads this common block to find the data to display. CONTROL BUTTONS The top of the Slicer's control panel has the following buttons: - Done Exits the Slicer. - Erase Removes all slices and draws an empty frame. - Undo Removes the most recently object by swapping the current view with the previous view. - Help Displays this help file. - Orientation Selects the orientation of the volume data with respect to the display axes. This button displays a sub-menu containing the following options: - XY Exchange Exchanges X and Y Axes - XZ Exchange Exchanges X and Z Axes - YZ Exchange Exchanges Y and Z Axes - X Reverse Reverses the X Axis - Y Reverse Reverses the Y Axis - Z Reverse Reverses the Z Axis - Reset Reverts to the default orientation - Interpolation Turning Interpolation On selections bilinear interpolation sampling, turning it Off selects nearest neighbor sampling. Bilinear interpolation is slower but yields more pleasing results. MODES The Slicer has the following modes: - Slices Displays or removes orthogonal or oblique slices through the data volume. - Block Displaces the surfaces of a selected block inside the volume. - Cutout Cuts blocks from previously drawn objects. - Isosurface Draws an isosurface contour. - Probe Displays the position and value of objects using the mouse. - Colors Manipulates the color tables and contrast. - Rotations Sets the orientation of the display. - Journal Records and plays back sessions. Select a mode by clicking on the appropriate button in the group of exclusive buttons near the top of the Slicer control panel. OPERATION OF EACH MODE The look of the Slicer control panel and the operation of the mouse buttons changes depending on the mode selected. - Slices Mode This Slicer control panel displays a representation of the data cube, showing the orientation and position of the selected slice. A row of buttons below this representation allow you to choose between "Draw" and "Expose" modes, and between Orthogonal and Oblique slices. - Draw mode displays the selected slice on the data cube, whether or not any slices or surfaces are already displayed. - Expose mode cuts the selected slice from a previously displayed surface. - Orthogonal slices are parallel to the faces of the data cube. - Oblique slices are not parallel to the faces of the data cube. Orthogonal slices are positioned within the data cube using the mouse: - Press and hold the left mouse button and drag the mouse cursor perpendicular to the current slice orientation to position the new slice. Releasing the mouse button draws the slice. - Click the middle mouse button within the data cube to display the 3D location and data value of the selected point. This information is displayed at the bottom of the Slicer control panel. - Click the right mouse button within the data cube to change the orientation of the slice plane. Oblique slices are defined by selecting a point inside the data cube, the angle between the X axis and the slice plane (the azimuth), and the angle between the Z axis and the slice plane (the elevation). When Oblique slices are selected, buttons allowing you to select azimuth or elevation are displayed in the window with the data cube. - To select the point, press and hold the left mouse button and drag the mouse cursor along the three visible faces of the data cube. - To select the azimuth, click on the "Azimuth" button at the top of the window containing the data cube, then manipulate the angle by pressing and holding the right mouse button while moving the mouse cursor from left to right. - To select the elevation, click on the "Elevation" button at the top of the window containing the data cube, then manipulate the angle by pressing and holding the right mouse button while moving the mouse cursor from left to right. Create the slice by setting the parameters and pressing the "Go" button at the top of the window containing the data cube. The values of the data parameters are displayed at the bottom of the Slicer control panel. - Block Mode This Slicer control panel displays a representation of the block that will be selected, along with several buttons controlling action in this mode: - GO button Draws the selected block. - Cancel button Removes the currently-defined block from the data cube. - Cut Into button Has no effect in this mode. - Cut Over button Has no effect in this mode. The representation of the block shows corners marked "0" and "1". Create the block to be drawn using the mouse: - Press and hold the left mouse button to position corner 0. Note that movement is constrained to the plane indicated by the colored grid in the center of the block. Lines are drawn from the selected corner to the three closest visible faces of the data cube. - Press and hold the middle mouse button to position corner 1. Note that movement is constrained to the plane indicated by the colored grid in the center of the block. Lines are drawn from the selected corner to the three closest visible faces of the data cube. - Click the right mouse button within the data cube to change the orientation of the plane. - Cutout Mode This Slicer control panel is identical to Block Mode, and blocks are selected in the same manner. In Cutout mode, selecting the "Cut Into" button means that only cuts in to a previously drawn object (an isosurface, for example) will be displayed. Selecting "Cut Over" means that the entire back faces of the selected block will be displayed, even if there is no object displayed in the data cube. - Isosurface Mode This Slicer control panel displays a histogram of voxel data versus population. Select the isosurface threshold either by adjusting the slider or by clicking (with any mouse button) in the histogram window. Two buttons allow you to choose whether the high or low side of the isosurface is displayed. If the higher voxel values are inside the isosurface, select the "Low Side" button, if the lower voxel values are inside, select the "High Side" button. Click the "GO" button to draw the isosurface. WARNING: this may take a long time, depending upon the size of the volume and the speed of your computer. - Probe Mode Click with any mouse button over the displayed data. The 3D location and data value are displayed at the bottom of the Slicer control panel. - Colors Mode This Slider control panel displays a pulldown menu and three sliders: - Color Tables menu Click on the "Color Tables" button to display a menu of color tables to apply. Click on a color table name to select that table. - Contrast Minimum/Maximum sliders Set these sliders to select the low and high data values that are displayed at the extremes of the color table. Both values are expressed as a percentage of the maximum voxel value. Increasing the minimum value or decreasing the maximum value increases the contrast. - Differential Shading slider Slices are differentially shaded to give and illusion of depth. Set this slider to 100% to determine the shading exclusively by the orientation of the slice. Set this slicer to 0% to determine the shading exclusively by the data value. - Rotations Mode This Slicer control panel allows you to change the orientation of the viewing cube. Note that changing the orientation erases any previously drawn slices or surfaces. - X Axis Rotation Positive values rotate the top of the data cube toward the viewer. - Z Axis Rotation Positive values rotate the base of the cube counter-clockwise. - Z Aspect Ratio This ratio affects the height of the data cube in relation to the size of the base. Values greater than 1 create a tall, narrow data area, values less than one create a short, wide data area. - Journal Mode This Slicer control panel allows you to record or play back files containing Slicer commands. To record a series of Slicer operations, specify a file to contain the recorded commands. (Note that if the specified file already exists, it will be overwritten.) Click "Start Recording," then perform any series of Slicer operations. When you have finished, click the "Stop Recording" button to close the journal file. To play back a file of recorded slicer commands, specify the file name and click "Playback." TRANSPARENCY The Transparency slider, located at the bottom of the Slicer control panel, sets a transparency threshold as a percentage of the maximum data value. If this slicer is set to either 0% or 100%, transparency is inactive. Voxel values less than the threshold value are not displayed if transparency is turned on. This slider has no effect when drawing isosurfaces.