Slicer Window

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
Hot Keys
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:

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.
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.
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 Up and Down Arrows step the zoom factor up or down.
The Zoom text box shows the current zoom and allows you to type in intermediate zoom factors.
The Checkerboard button toggles between fast rendering (nearest neighbor interpolation) and slower but higher quality image rendering (cubic interpolation for zooms greater than 1, antialiased filtering for zooms less than 0.75).
The Lock button will keep the image on the same slice even when the current Z value is changed in another window; and conversely, a locked Slicer can be moved perpendicular to the slice without affecting the current Z value for other windows. In classic mode, the image is also locked to the current position, even when drawing model points. In addition, a locked Slicer in classic mode responds to the image movement keys (arrows and PageUp/PageDown) by moving the current point by one pixel in directions parallel or perpendicular to the plane of the slice - the same behavior as in the new mode.
The Centering button toggles between the new mode of window behavior and having the image always centered on the current model point unless locked (classic mode).
The Rubber band button allows you to draw a rectangular box that can be used for extracting a rotated subvolume from the file, defining the area for a snapshot, or resizing the window to a selected area. See the section on Using the Rubber Band below.
The Arrow button allows you to draw an arrow quickly for pointing out a feature in the image. Press the button, then move the mouse to the desired position for the tail of the arrow, press the first mouse button, and hold it down while positioning the head of the arrow. The arrow can be drawn only at the current rotation angles, so it is turned off if you change the angles. The arrow will stay at the same image position if you pan the image. It will also stay in the same position in the window if you step through planes parallel to the slice with PageUp and PageDown in this Slicer window, but not if you step through Z elsewhere. Turn off the button to remove the arrow. If you want to draw multiple arrows, open the Grab with Note plugin under the Special menu.
The FT button toggles between displaying the image slice or its Fourier transform. The entire image in the whole window, including any gray borders, is padded into a square array, then the boundaries of the actual image are tapered down to match any gray borders. This image is Fourier transformed, then the portion that fits is drawn in the window. Thus a non-square window will give a transform that is isotropic in X and Y, but portions will be not be visible in one of the dimensions, so use a window that is near square to see all of the transform. Zooming down below 1 changes the scale of the transform: low frequencies show up farther from the origin and high frequencies disappear as a result of subsampling the image. Zooming up does not change the scale of the transform for zooms above 1; it just decreases the number of pixels that the transform is based on. To see the transform at a higher zoom, increase the zoom and increase the window size by the same amount. High-resolution mode will sample pixels with accurate interpolation without changing the number of pixels that the transform is based on.
The Z-Scale button lets you control whether the volume will be displayed with Z-scaling. If you turn Z-scaling on, then the volume will be scaled before it is rotated and sliced, and thus the rotation angles will not select the same slice as with no Z-scaling. These angles will be correct in a Z-scaled volume, but would not be correct for using Rotatevol to achieve the same rotation of the original volume.
When images are loaded in with a different binning in Z versus X and Y, the angles are correct for the original, unbinned volume. This is accomplished by applying an implicit Z scaling.
The Show slice button will cause lines to be drawn in the XYZ and ZaP windows to show the intersection of the current slice.
The Contour button (C) will find the plane that best fits the current contour and set the X and Y angles and center position to show that plane.
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. This is necessary to get a complete image when angles are not zero. However, only full-resolution data are loaded, not reduced data, even if the zoom is less than 1. Moreover, data are loaded for all Z values, not just the ones needed to fill in the current display. Thus, this loading can take quite a while, especially if the window is displaying a large number of unbinned pixels. Loading is asynchronous, so other actions can be done while it is happening, and intermediate amounts of image, or even the full image, may appear if you do so. The display is not updated automatically when the data are done being loaded.

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 an 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, up to about 20 by default. This limit can be set in the Look & Limits panel of the 3dmod preferences dialog. 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. If there are more image files than windows opened, the first window will be set to the current time rather than time 1. In this case, stepping time in one of the linked Slicers will make all of them step in tandem so as to display the next set of times. For example, if there are 20 Slicers displaying times 1 to 20, stepping up will make them show 21 to 40.

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:

Save saves the angles and position in the current row of the table, or into a new row if there are no rows in a table.
New saves the angles and position into a new row in the table.
Set sets the angles and position from the current row of the table.
Auto selects an automatic (continuous) update of the current row of the table from changes in this Slicer. When this option is off, angles are saved only when Save is pressed. The Slicer is set to an angle only when either the Set toolbar button or the Set Angles button in this window is pressed. When the option is on, angle or position changes in a Slicer automatically modify the stored values that are shown in the current row. Changing the current row of the table will set the angles in the active Slicer. When the time is changed, the Slicer is automatically set to the current values for the new time (which can be in a different row of the table). In addition, if you edit one of the cells, the values in that row are sent to the Slicer. When this option is turned on, neither the Slicer position nor the angles in the table are changed because it is not known which action you desire - it is up to you to sychronize the angles in the table with the Slicer window one way or the other.

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:

First Button Drag: Pan the slice image relative to the center point (but not in Classic mode).
Shift-Second Button Drag or Second Button Drag with Sh ("Shift lock") on: Rotate the volume around an axis in the plane of the slice and perpendicular to the direction of mouse movement, as in the model view window.
Shift-Third Button Drag or Third Button Drag with Sh on: Rotate the currently displayed slice about its center by rotating the volume around an axis perpendicular to the slice.

In movie mode, the buttons do the following:

First Button Click: Set the current image point, which affects the display in other windows. (Classic mode: set the current viewing point of the Slicer as well.)
Ctrl-Second Button: Start movie forward, perpendicular to viewed slice
Ctrl-Third Button: Start movie backward, perpendicular to viewed slice

In model mode, the buttons do the following:

First Button: Attach to the nearest model point, or detach from the current contour. For open and closed contours, only points within 0.5 pixel of the current plane will be considered, even if more of the model shows up because the thickness for model display is set higher than 1. Spherical points can be selected from nearly any plane on which they are visible. 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.
Second Button Click: (if Sh not on) Insert a point after the current point. This button can be held down to insert points continuously. (Classic mode: continuous tracing only works with the window position locked.) A new contour will be started automatically after a change in the slice angle or the position perpendicular to the slice, if you are modeling either closed contours or open contours in an object with the option set to start new contours automatically at new Z values.
Third Button Click: (if Sh not on) Move the current model point to the selected location

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.

-/= Decrease/Increase zoom (Keypad - and + also decrease/increase zoom)
_/+ or Keypad - Decrease/Increase displayed image thickness
9/0 (Keypad Shift - and Shift + also do this Decrease/Increase displayed model thickness
L Show slice in ZaP and XYZ windows
K Toggle keeping slice centered on current point (classic mode)
Shift+B Toggle the rubber band on or off
Shift+F Toggle between showing the image and showing the FFT of the image
Shift+R Resize the window to the area enclosed in the rubber band and turn off the band
Ctrl+Shift+R Resize and center the area enclosed in the rubber band to fill the window in one dimension.
S Save model to file
Ctrl+S, Shift+S or Ctrl+Shift+S saves the Slicer window, or the area inside the rubber band, into a TIFF file, a file in the primary non-TIFF format, or a file in the second non-TIFF format
X/Y/Z Align current and previous model points along X, Y or Z axis
Shift+X/Shift+Y/Shift+Z Align first and last points of contour along X, Y or Z axis
Shift+W Change X and Y angles so that the current contour is flat in the slice.
Q Report distance in 3D between the current model or image point and the point under the mouse cursor. The current image point is used in Movie Mode or if there is no current model point. If the current point appears in a bright color, it is on the plane being displayed, and the distance corresponds to a line length in the plane of the image. If pixel size varies among the sections or among multiple image files, the measurement will be based on the pixel size of the program's current section and time. See Variable Pixel Sizes for details.

Arrow Keys When not in Classic Mode, the arrow keys shift the image in the direction of the key by one pixel. Ctrl and an arrow key will shift the image in 0.2 pixel steps, which is useful for setting the center of rotation more precisely. In Classic Mode, the arrow keys shift the current image point in the direction of the arrow, and since the current point stays centered, the image shifts in the opposite direction.

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

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

With Shift key down or Sh on, rotate volume:

4/6 (Left/Right) Rotate volume around Y axis in plane of viewed slice
2/8 (Down/Up) Rotate volume around X axis in plane of viewed slice
9/3 (PgUp/PgDn) Rotate in plane of displayed slice
</> Decrease/Increase increment for these rotations; the increment can be 0.1, 0.3, 1, 3, 10, 30 or 90 degrees and it starts at 1 degree. With Sh on, ,/. also change the increment.

Using the Rubber Band

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

To start the rubber band, press the toggle button or use the Shift+B hot key. Press the first mouse button at any corner of the desired box and hold the mouse down while dragging to the opposite corner.
After you draw it initially, you can resize or move the rubber band by bringing the mouse near an edge or corner. The cursor will change to a horizontal or vertical double arrow to indicate that you can move one side, or to a diagonal double arrow to indicate that you can move one corner. Press the first mouse button and drag to adjust the size, or press the second mouse button and drag to shift the band without changing its size.
Whenever you are resizing the band, its dimensions in window pixels are shown in the general toolbar, in place of the Lo and Hi buttons. To see the size temporarily without changing the band, position the cursor over any edge and press the first mouse button without moving the mouse.
A non-montaged snapshot will capture the area inside the rubber band.
The hot key Shift+R will resize the window to show the area enclosed by the rubber band, and turn off the band. The hot key Ctrl+Shift+R will zoom the area in the rubber band and shift it so that it fills the window in one dimension.
"Extract File" in the Edit menu will run Rotatevol to extract the region defined by the rubber band, after limits in the third dimension have been set with the Lo and Hi buttons in the General toolbar. Go to one end of the desired range with PageUp/PageDown or the View axis position slider, and press one of the buttons. Go to the other end of the range and press the other button. These buttons initially appear as red to indicate that no limits have been set and turn green when a limit is set. However, it is possible to adjustthe band size or position after setting limits. A button turns yellow if a set limit can no longer be reached, in which case extracting will include fewer slices. If you hold down the Shift key and click on a button, it will return to the limiting slice or go to the last slice that can be reached.
If there are multiple Slicers with rubber bands, the volume is extracted based on the area defined in the most recently active window. If there is both a Zap and a Slicer with rubber bands, File - Extract File runs an operation as specified by the band in the most recently active window.

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:

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.
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.
Model a contour by clicking or dragging with the second mouse button.
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.
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).
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.
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:

If there are multiple processors in your system, the Slicer uses multiple threads executing simultaneously to compute the image. By default, the number of threads is the number of processors detected in the system, and the speedup will be nearly linear with the number of processors. If the environment variable IMOD_PROCESSORS is set, it will set the number of threads to the value of this variable instead.
When you pan or rotate the image with the mouse, the Slicer will evaluate the number of voxels that needs to be computed and, if necessary, turn off the high quality interpolation and reduce the number of slices to keep the computation time reasonable. This behavior is controlled by a limiting number of voxels that can be adjusted in the Look/Limits tab of the 3dmod Preferences dialog. If you find the Slicer too sluggish when using the mouse with averaged slices, reduce the value; if you want to keep it from reducing the quality as much as it does, increase the value.
This dynamic reduction in quality will not occur when dragging the angle sliders, unless you check the box to apply the voxel limit to this operation as well in the Look/Limits tab of the 3dmod Preferences dialog.
The evaluation of computation time is divided by the number of processors, with the result that it reduces the quality at a higher number of voxels when there are more processors.

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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