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.


Window Behavior and Classic Centering Mode
The First Toolbar
The Second Toolbar
The Time Toolbar
The Angle Saving Toolbar
Mouse Actions and Movies
Hot Keys
Modeling Tilted Contours to be Meshed

Window Behavior and Classic Centering Mode

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 First Toolbar

The Second 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.

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

On the 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

If multiple image files have been loaded into 3dmod, an additional toolbar appears, identical to 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.

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

All mouse buttons behave as 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 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


-/=        Decrease/Increase zoom
_/+       Decrease/Increase displayed image thickness
9/0       Decrease/Increase displayed model thickness
s         Show slice in ZaP and XYZ windows
k         Toggle keeping slice centered on current point (classic mode)
Ctrl-S   Snapshot to TIFF file
Shift-S   Snapshot to primary type of non-TIFF file
Ctrl-Shift-S   Snapshot to second type of non-TIFF file
x/y/z    Align current and previous model points along X, Y or Z axis
X/Y/Z   Align first and last points of contour along X, Y or Z axis
W        Change X and Y angles so that the current contour is flat in the slice.

Numeric Keypad:
4/6 (Left/Right)    Decrease/Increase last adjusted angle by 0.1 degree
2/8 (Down/Up)     Decrease/Increase last adjusted angle by 0.5 degree
1/3 (End/PgDn)   Decrease/Increase last adjusted angle by 15 degrees
0 (Insert)             Set last adjusted angle to 0

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. 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.
  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.
  5. To model another area at a different orientation, be sure to start a new surface (use the 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 W hot key or the C button in the first toolbar to reorient to the contour, then step to the desired slice. Using 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.
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.

Help Index