The Slicer Window

The slicer allows you to display a slice at an arbitrary angle through the volume, centered around a selected point. This center of rotation is always displayed in the center of the window. Multiple slices can be averaged. Modeling can be done.

Slicer has two to four dockable toolbars that may be floated as separate windows so that the image will fill the entire window area. When they are floated, they will still pass hot keys on to the slicer window.

Angles, Window Behavior and Classic Centering Mode
The General Toolbar
The Slice Control Toolbar
The Time Toolbar and Linked Slicers
The Angle Saving Toolbar
Mouse Actions and Movies
Using the Rubber Band
Modeling Tilted Contours to be Meshed
Managing Slicer Performance

Angles, Window Behavior and Classic Centering Mode

The orientation of the slice is governed by the Z, Y, and X rotation angles, which are applied in that order to rotate the volume before slicing. These angles can be set directly with sliders, or by using the numeric keypad to change the angle last adjusted by a slider by small or large increments. Once angles become large, however, the overall effects of changes in the Z or Y angles become unintuitive. An alternative way to control the slice orientation is to rotate the volume relative the axes in which it is currently viewed. With the Shift key held down, mouse buttons and keypad keys can be used to rotate the volume just as a model can be rotated in the Model View window. The X, Y, and Z angles will change to accomplish the desired rotation. There is also a toolbar button that works as a "Shift lock" so that the Shift key does not need to be held down.

The behavior of the slicer was changed in IMOD 3.10.10 so that it works more like the Zap window. The old behavior of the window is called "Classic mode", and there is a toolbar button as well as a hot key to switch to this mode. The principal differences are:

  1. In the new mode, the image can be panned with the first mouse button, and clicking in the window changes the current image or model point without changing the center of rotation, or shifting the image. In classic mode, the image cannot be panned, and clicking in the window or changing the current point in another window recenters the image on the selected point unless the slicer window is locked.
  2. In the new mode, arrow keys pan in the plane of the slice, while the PageUp and PageDown keys move the center of rotation perpendicular to the plane of the slice. The Page keys will also move the current point in Z by an amount that will keep a Zap window in sync with the slicer. In classic mode, the arrow keys and PageUp and PageDown move the current point in X, Y, and Z regardless of the orientation of the slice, unless the slicer is locked.
  3. In the new mode, the slicer will respond to some but not all changes in the current point by moving its center point. Specifically, it will change the Z of its center point when only the Z of the current point changes, as would be produced by changing Z in another window. It will change the X or Y of its center point by 1 when X or Y of the current point changes by 1, as would be produced with arrow keys in other windows. Again, in classic mode, the center point is kept the same as the current point unless a slicer is locked.
Although the new mode should be more convenient in general, classic mode is still useful, such as for keeping the slicer synchronized with the current point being displayed in other windows, or for keeping the current model point visible while stepping through a contour. In addition, if one wants to see the current point and it is not visible in the slicer, one can simply toggle the mode on and off again to center the current point.

The General Toolbar

The Slice Control Toolbar

On the left are three sliders with which you can adjust the rotations about the X, Y, and Z axes. The rotation angles are applied to the volume, not to the slicing plane, and they are applied in the order Z, Y, X; thus these same angles can be used directly in other programs that rotate the volume. Clicking a slider with the left mouse button will change the angle by 1 degree; clicking with the middle button moves the slider immediately to the position of mouse. If you drag the slider, the representation of the slice in the data volume will change continuously, and the image will also be updated if the slider is continuously active. If the slider is not continuously active, the image will not be updated until you release the slider. Typically the sliders will be continuously active unless you press the Ctrl key, although you can change this default behavior in the 3dmod Preferences dialog, accessed through the Edit-Options menu entry.

A fourth slider at the bottom, View axis position shows the position of the slice along the axis perpendicular to the current plane, and allows you to riffle through the planes along that axis.

In the middle is a cluster of buttons for rotating the volume around the viewer's X, Y, and Z axes. The arrow buttons provide a substitute for using the numeric keypad with the Shift key held down. If one of these buttons is held down, repeated steps are taken. The Shift lock button in the middle of the arrows (Sh) toggles a mode in which the second and third mouse buttons and numeric keypad keys operate as if the Shift key were held down. The + and - buttons increase and decrease the angular step when using the rotation buttons here or the numeric keypad in shifted mode.

In the upper right is a representation of the slice that is being cut from the data volume.

In the bottom right are controls for adjusting the thickness of the image slice and the thickness of model that is shown on the slice.

The Time Toolbar and Linked Slicers

If multiple image files have been loaded into 3dmod, an additional toolbar appears, with the same controls as the toolbar in the Zap window. The Time lock button will prevent changes in other windows from changing the time (image file) displayed in this slicer; and conversely this slicer's time can be changed without affecting other windows. The left and right arrows will step backward and forward in time.

In addition, the time toolbar has a Link checkbox that will make all the Slicers with this option checked have the same angles, zoom, and image thickness. They will also have the same position unless one of their position Lock buttons is on. This option can be used together with the Time lock button to get synchronized displays of several volumes in separate Slicers.

The Image - Linked Slicers menu entry will open a complete array of linked slicers, one per image file and each one already locked to a time. The slice control toolbar will be detached and moved to the top or left side for the first window and hidden for the other windows. (It is placed in the middle of the top or left to keep it from being lost if there are two side-by-side monitors of unequal size.) The windows will be arranged in rows and shrunk by up to 50%, if necessary, to fit as many as possible. If the Link box is turned off for a slicer, its toolbar will be restored. If the first window is closed or its Link is turned off, another window's toolbar will be moved to the top or left. You can press the close button on the detached toolbar window to close all of the linked slicers.

The Angle Saving Toolbar

Slicer angles and center positions can be saved in the IMOD model by opening the Slicer Angles dialog box, using the Edit-Angles menu entry. When this dialog box is opened, all slicers will acquire an additional toolbar with the following controls:

Mouse Actions and Movies

The actions of the mouse buttons are similar but not identical to those in the Zap and XYZ windows. In classic mode, unless the image position is locked by the lock button, the first mouse button in movie mode, and all mouse buttons in model mode, will change the current viewing point in the data volume.

In either movie or model mode, moving the mouse with a button held down does the following:

In movie mode, the buttons do the following:

In model mode, the buttons do the following:

By default, these buttons correspond to the left, middle, and right buttons, but you can change these assignments in the 3dmod Preferences dialog.

When a movie is started with an obliquely oriented slice, the range of the movie is determined by two sets of limits. One set of limits is imposed to keep the central displayed point within the data volume. The other limits are based on the starting and ending movie limits for the axis that is closest to perpendicular to the slice. These limits are set in the 3dmod Movie Controller (opened with Edit - Movies...). The slice angles can be changed while movieing and these limits will be adjusted dynamically.

Hot Keys

Most of these hot keys, and many others, are available in a menu that pops up when you right-click over any of the Slicer toolbars.

Numeric Keypad:
With no Shift key and with Sh ("Shift lock") not on, manipulate the X, Y, or Z angles:

With Shift key down or Sh on, rotate volume:

Using the Rubber Band

The rubber band is used to enclse a rectangular area just as in the Zap window, although it has fewer uses in the Slicer.

Modeling Tilted Contours to be Meshed

It is possible to mesh contours that have been modeled at an oblique orientation in the slicer, provided that all of the contours in a surface are at the same orientation, and that the contours are properly spaced apart. By default, the slicer will automatically start a new surface at the same time as it starts a new contour when it detects that the slicer angles have changed enough from the angles at which the current contour was drawn. This behavior can be turned off with an option in the 3dmod Preferences dialog (menu entry Edit - Options). If you are going to model at multiple angles, it is advisable to open the Surface-Contour-Point dialog to monitor the surface number (menu entry Edit - Surface - Go to).

To model tilted slices, follow these procedures:

  1. Select an area to model and center it in the window. You may wish to lock the slicer to keep other windows from affecting its position.
  2. If there are already contours in this object, start a new surface with N or allow the slicer to start the new surface for you.
  3. Model a contour by clicking or dragging with the second mouse button.
  4. Step between slices with the PageUp and PageDown keys in this slicer. Start new contours in the same surface with n, or rely on new contours starting automatically.
  5. If you start modeling another area at a different orientation, the slicer should start a new surface automatically. Otherwise, you can start a new surface manually (use the Shift+N hot key instead of N).
  6. To return to modeling a surface after changing the angles, or after the plane of the data has been changed by stepping in Z in another window, select one of the existing contours with the first mouse button. Press the Shift+W hot key or the C button in the first toolbar to reorient to the contour, then step to the desired slice. Using Shift+W is very important, not just for getting the same angles, but also for getting back to the exact coordinates to preserve the spacing between slices. An alternative is to store the angles and position of one slice with the Slicer Angles dialog.
  7. If you go back to modeling in a Zap or XYZ window after modeling tilted slices, be sure to select an existing planar contour in that window before making a new contour or starting to draw. This will keep you from appending to a tilted contour or from getting an inappropriate surface number for the new contour.
Note that if you model at intervals of more than one pixel, it is not so important to preserve the spacing between slices as just described.

Managing Slicer Performance

The time that the slicer takes to compute a new image depends on three factors: the size of the image window, the number of slices being averaged, and whether high quality interpolation is selected. For large windows and many slices, the computation time could take hundreds of milliseconds. The slicer uses several methods to manage the computation time, and you can affect them, as follows: In general, whenever performance is an issue, it is advisable to keep the size of the slicer window to just what is needed to examine the area of interest.

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