Basic Features of the XYZ Window
The Tool Bars
Hot Keys Special to the XYZ Window
Mouse Button Function in Movie Mode
Mouse Button Function in Model Mode
Marker Lines
Modeling Meshable Contours in XZ and YZ Planes

Basic Features of the XYZ Window

When an image plane is too large to fit in its view box, the image can be panned with the first mouse button. The windows do not all pan independently; there are just three underlying pan offsets, for X, Y and Z, so that when you pan, two windows will usually move together to keep corresponding regions of the volume visible.

For volumes that are much larger in X and Y than in Z, the allocation of the window space among the three view boxes can be changed by dragging the light blue square, at the intersection of the X and Y marker lines. This square will move along a diagonal so as to keep the Z sizes of the XZ and YZ view boxes the same.

Modeling in the XYZ window is very similar to the basic modeling that can be done in the Zap window, except that it can be done in any of the three planes.

The Tool Bar

• The up and down arrows step the zoom factor up or down.
• The zoom edit box shows the current zoom factor and allows one to type in a custom zoom.
• The checkerboard button toggles between fast rendering and slower but higher quality interpolated image rendering. When the zoom is below 0.75, the higher quality display uses a filter to remove aliased information, which often appears as extra noise.
• The lock button will keep the display at the current location (and time, if multiple image files are loaded), regardless of changes in the global current point. With this button on, changes in the display of this window (using the sliders, PageUp, PageDown, the arrow hot keys, or 1 or 2 hot keys to change time) will not affect the global current point and the display in other windows. Unlike in the Zap and Slicer windows, both image position and time are locked by this single button.
• The Z-scale button toggles between displaying voxels at the same scale in Z as in X and Y, and displaying them stretched by the model's Z-scale. The state of this button is saved between sessions. Once this setting is turned on, a new XYZ window will open with the boxes apportioned appropriately. The Z-scale can be set in the Model Header dialog, opened with Edit-Model-Header.
• The centering button will pan the images to bring the current point as close as possible to the center of each view box. The centered point is either the current image point in movie mode or the current model point in model mode.
• The fill cache button appears if 3dmod is opened with an image pyramid and can be used to load data into the cache for the currently displayed X/Y region at the current zoom. This is necessary to get a full image in the XZ and YZ panels. Data are loaded for all Z values, not just the ones visible in those panels. Loading is asynchronous, so other actions can be done while it is happening, and intermediate amounts of image may appear if you do so. The display is not updated automatically until the data are all loaded.
• The Sum spin box allows summing (averaging) of the selected number of planes of data. If a cache is being used, all Z planes needed for the sum in the XY panel will be loaded if necessary, but the display may be incomplete in the XZ and YZ panels. If 3dmod is opened with an image pyramid, the sum is computed just for the region being displayed, and panning may be slow if many slices are being averaged. Otherwise, the program computes the sum over the full slice in each plane, which means that panning will be fast because it can use existing sums, but other operations may be slow with large volumes or with many slices being averaged. Summing is not available for RGB data.
• The X slider allows one to change the X location.
• The Y slider allows one to change the Y location.
• The Z slider allows one to riffle through images or select a particular section to display.

• K will pan the images to bring the current point as close as possible to the center of each view box, just as with the centering toolbar button.
• R toggles between fast rendering and slower but higher quality interpolated image rendering.
• Shift+P Toggles the projection of the current contour onto the side views. Scattered point objects are always displayed in all three views.
• Q Reports the distance between the mouse and the current image or model point, if the mouse is in one of the three view boxes. The current model point is used in Model Mode, if one is defined. Otherwise, distance is measured to the current image point in this XYZ window (which may be different from the global current image point). A 3D distance is reported, althoughly typically it will be the same as the 2D distance in the plane.
• Ins on the keypad: In model mode, this key works the same as the second mouse button. A single keystrike adds one point; holding the key down allows points to be added continuously.
• Arrows and PageUp/PageDown: These keys move the current viewing point relative to the plane in the box where the mouse is located, or relative to the XY plane if the mouse is not over a box. For example, when the mouse is over the XZ box, the Up arrow advances in Z and PageUp advances in Y, which switches to the next XZ plane. This is useful when modeling in the XZ or YZ planes.
• Keypad Arrows and PageUp/PageDown: In model mode, the numeric keypad arrow keys move the current model point laterally and PageUp/PageDown move it between slices, relative to the plane in the box where the mouse is located. If the latter keys make a planar contour non-planar, a warning will be issued, because as long as this contour is the current one, new contours will not be made automatically when switching to a new plane or slice.
• ESC will close the XYZ window.

• First Button Click: Select the current image point, marked by a small cross in the three planes. In one of the three view boxes, this will change the coordinates displayed in the other two planes. Clicking in the horizontal gutter region occupied by the green marker line will change the current X coordinate and the YZ plane. Clicking in the vertical gutter region will select a new Y coordinate and XZ plane. Clicking in the upper right region will select a new Z coordinate and XY plane, as indicated by the crossed marker lines.
• First Button Drag: In one of the three view boxes, this pans an image if it is larger than its view box. In the horizontal or vertical gutter or the upper right region, this riffles through YZ, XZ, or XY planes, respectively. On the small blue square at the intersection of the marker lines, this adjusts the allocation of window space among the view boxes.
• Second Button Click: In one of the three view boxes, start movie through the planes in the forward direction, or stop movie,
• Third Button Click: In one of the three view boxes, start movie through the planes in the backward direction, or stop movie.

• First Button Click: In any of the slice view boxes, this makes the nearest visible model point be the current model point. If there is no point nearby, it detaches from the current point and contour and selects a current viewing point instead. Elsewhere, this click behaves as in movie mode. To attach to points in any object, including ones that are turned off, there is an option in the Behavior panel of the 3dmod Preferences dialog.
• First Button Drag: Pans images or riffles through planes, just as in movie mode.
• Second Button Click: In any of the view boxes, adds one point to the current contour or starts a new contour when modeling planar contours and the new point would make the current contour nonplanar. The latter occurs when modeling a closed contour object or an open contour object with Start new contour at new Z selected in the Edit-Object-Type dialog.
• Second Button Drag: In any of the view boxes, continually adds points to the current contour as the mouse is moved.
• Third Button Click: In any of the view boxes, modifies the current model point to be at the selected position.
• Third Button Drag: In any of the view boxes, continually modifies points as the mouse is moved. This only works when the current model point is in the interior of the contour, not at its end.

• Cross-hair (upper right corner): moves the current point in Z on the visible portion of the image.
• Horizontal slider (between top and main window): moves the current point in X on the visible portion of the image.
• Vertical slider (between top and main window): moves the current point in qY on the visible portion of the image.

• The meshing code is able to connect contours that not in the XY plane when they are all assigned the same surface number, and when that surface contains only contours that lie in parallel planes.
• When you start modeling a closed contour in one of the boxes, 3dmod will change the surface number of the contour, if necessary, to make sure that the surface consists only of contours in parallel planes. This happens both when you create a new contour before starting to draw, and when the program automatically creates a new contour for you. This behavior can be turned off with an option in the Behavior tab of the 3dmod Preferences dialog.
• The same features can operate when you model open contours, but only if you select Start new contour at new Z in the Edit-Object-Type dialog.
• If you do not manipulate surface numbers or start a new surface yourself, typically contours modeled in the XY plane will be in surface 0, ones in the second plane that you model will be in surface 1, and ones in the other plane will be in surface 2.
• You can still start new surfaces if you wish to use surfaces to keep track of different structures.
• If you start modeling in a Zap window when the current contour was drawn in the XZ or YZ plane, 3dmod will recognize that the current surface is inappropriate and change to one appropriate for modeling in the XY plane. This is not the case when returning to drawing in a Zap window after drawing tilted contours in a Slicer window.
• It is a good idea to open the Surf/Cont/Point dialog (e.g., with Edit-Surface-Go To) to monitor surface numbers. You can also visualize all of the contours in each surface by opening the Model View window and selecting Current surface only in the Subsets panel of the Edit-Objects dialog.

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