User Interface

Application overview

Slicer stores all loaded data in a data repository, called the “scene” (or Slicer scene or MRML scene). Each data set, such as an image volume, surface model, or point set, is represented in the scene as a “node”.

Slicer provides a large number “modules”, each implementing a specific set of functions for creating or manipulating data in the scene. Modules typically do not interact with each other directly: they just all operate on the data nodes in the scene. Slicer package contains over 100 built-in modules and additional modules can be installed by using the Extensions Manager.

Module Panel

This panel (located by default on the left side of the application main window) displays all the options and features that the current module offers to the user. Current module can be selected using the Module Selection toolbar.

Data Probe is located at the bottom of the module panel. It displays information about view content at the position of the mouse pointer.

Views

Slicer displays data in various views. The user can choose between a number of predefined layouts, which may contain slice, 3D, chart, and table views.

The Layout Toolbar provides a drop-down menu of layouts useful for many types of studies. When Slicer is exited normally, the selected layout is saved and restored next time the application is started.

Application Menu

  • File: Functions for loading a previously saved scene or individual datasets of various types, and for downloading sample datasets from the internet. An option for saving scenes and data is also provided here. Add Data allows loading data from files. DICOM module is recommended to import data from DICOM files and loading of imported DICOM data. Save opens the “Save Data” window, which offers a variety of options for saving all data or selected datasets.

  • Edit: Contains an option for showing Application Settings, which allows users to customize appearance and behavior of Slicer, such as modules displayed in the toolbar, application font size, temporary directory location, location of additional Slicer modules to include.

  • View: Functions for showing/hiding additional windows and widgets, such as Extensions Manager for installing extensions from Slicer app store, Error Log for checking if the application encountered any potential errors, Python Interactor for getting a Python console to interact with the loaded data or modules, show/hide toolbars, or switch view layout.

Toolbar

Toolbar provides quick access to commonly used functions. Individual toolbar panels can be shown/hidden using menu: View / Toolbars section.

Module Selection toolbar is used for selecting the currently active “module”. The toolbar provides options for searching for module names (Ctrl + f or click on magnify glass icon) or selecting from a menu. Module history dropdown button shows the list of recently used modules. Arrow buttons can be used for going back to/returning from previously used module.

Favorite modules toolbar contains a list of most frequently used modules. The list can be customized using menu: Edit / Application settings / Modules / Favorite Modules. Drag-and-drop modules from the Modules list to the Favorite Modules list to add a module.

Status bar

This panel may display application status, such as current operation in progress. Clicking the little X icons displays the Error Log window.

Review loaded data

Data available in Slicer can be reviewed in the Data module, which can be found on the toolbar or the modules list . More details about the module can be found on the Slicer wiki.

The Data module’s default Subject hierarchy tab can show the datasets in a tree hierarchy, arranged as patient/study/series as typical in DICOM, or any other folder structure:

The Subject hierarchy view contains numerous built-in functions for all types of data. These functions can be accessed by right-clicking the node in the tree. The list of actions differs for each data type, so it is useful to explore the options.

Medical imaging data comes in various forms and representations, which may confuse people just starting in the field. The following diagram gives a brief overview about the most typical data types encountered when using Slicer, especially in a workflow that involves segmentation.

Selecting displayed data

Data module’s Subject hierarchy tab shows all data sets in the scene. Click the “eye” icon to show/hide an item in all views. Drag-and-drop an item into a view to show it in that view.

Multiple items can be selected in the subject hierarchy tree using Ctrl-Left-Click or Shift-Left-Click and dragged at once into selected view. If two volumes are dragged into a view at the same time then they will be both shown, blended together.

If a view is displayed only in selected views, you can right-click on the item and select “Show in all views” to quickly show in all views.

If view link is enabled for a slice view then dragging a volume to any of the views will show the volume in all the views in that group.

Display options can be adjusted by right-clicking the eye icon in the display column of the tree. Note that these options are different from options that are offered when right-clicking on the “Node” or “Transform” column in the tree.

For volumes, display options include:

  • Reset field of view on show: if enabled, then showing a volume makes adjust views to show the volume in the center, filling the field of view.

  • Reset view orientation on show: if enabled, then showing a volume makes the slice views aligned with the volume axes.

Interacting with views

View Cross-Reference

Holding down the Shift key while moving the mouse in any slice or 3D view will cause the Crosshair to move to the selected position in all views. By default, when the Crosshair is moved in any views, all slice views are scrolled to the same RAS position indexed by the mouse. This feature is useful when inspecting.

To show/hide the Crosshair position, click crosshair icon .

To customize behavior and appearance of the Crosshair, click the “down arrow” button on the right side of the crosshair icon.

Mouse Modes

Slicer has multiple mouse modes: Transform (which allows interactive rotate, translate and zoom operations), Window/Level to adjust brightness/contrast of the image volumes, and Place (which permits objects to be interactively placed in slice and 3D views).

The toolbar icons that switch between these mouse modes are shown from left to right above, respectively. Place Fiducial is the default place option as shown above; options to place other nodes such as Ruler and Region of Interest Widgets are also available from the drop-down Place Mode menu.

Note: Transform mode is the default interaction mode. By default, Place mode persists for one “place” operation after the Place Mode icon is selected, and then the mode switches back to Transform. Place mode can be made persistent (useful for creating multiple fiducial points, rulers, etc.) by checking the Persistent checkbox shown rightmost in the Mouse Mode Toolbar.

Adjusting image window/level

Medical images typically contain thousands of gray levels, but regular computer displays can display only 256 gray levels, and the human eye also has limitation in what minimum contrast difference it can notice (see Kimpe 2007 for more specific information). Therefore, medical images are displayed with adjustable brightness/contrast (window/level).

By default 3D Slicer uses window/level setting that is specified in the DICOM file. If it is not available then window/level is set to contain the entire intensity range of the image (except top/bottom 0.1%, calculated using percentiles, to not let a very thin tail of the intensity distribution to decrease the image contrast too much).

Window/level can be manually adjusted anytime by clicking on “Adjust window/level” button on the toolbar then left-click-and-drag in any of the slice viewers. Optimal window/level can be computed for a chosen area by lef-click-and-dragging while holding down Ctrl key.

Additional window/level options, presets, intensity histogram, automatic adjustments are available in Display section of Volumes module.

3D View

Displays a rendered 3D view of the scene along with visual references to specify orientation and scale.

Default orientation axes: A = anterior, P = posterior, R = right, L = left, S = superior and I = inferior.

3D View Controls: The blue bar across any 3D View shows a pushpin icon on its left. When the mouse rolls over this icon, a panel for configuring the 3D View is displayed. The panel is hidden when the mouse moves away. For persistent display of this panel, just click the pushpin icon.

  • Center 3D view (small square) centers the slice on the currently visible 3D view content and all loaded volumes (even if volumes that are not visible). The field of view (zoom factor) is not adjusted, therefore it may be necessary to zoom in/out to see all objects. To reset the center and field of view at the same time, click in the 3D view and hit r key.

  • Viewpoint direction switches orientation of the view between standard directions. Clicking on Left, Right, Anterior, Posterior, Superior, Inferior button will make the 3D content viewed from that direction.

  • View link button synchronizes properties across 3D views (viewpoint position, direction, ruler, orientation marker, etc. settings).

  • Orthographic/perspective rendering mode toggle. Orthographic mode (parallel projection) is useful for assessing size, because displayed object size does not depend on distance from the viewpoint. Perspective mode provides better depth perception, because objects that are closer appear larger.

  • Ruler controls display of ruler. Only available in orthographic rendering mode.

  • Stereo viewing enables stereoscopic display. Red/blue and anaglyph modes just require inexpensive red/blue colored glasses. Other modes require special 3D display hardware. Note that SlicerVirtualReality extension offers superior stereo viewing and interaction experience, with fully immersive 3D visualization by a single click of a button, and rich interaction with objects in the scene using 3D controllers.

  • More options (…)

    • Use depth peeling must be enabled for correct rendering of semi-transparent surfaces (in models, markups, etc). It may make rendering updates slightly slower and artifacts when volume rendering is used in the view.

    • Show/Hide frames per second (FPS) displays rendering speed in the corner of the view.

  • Orientation Marker controls display of human, cube, etc in lower right corner.

  • Visibility options controls visibility of view background color and displayed components.

  • Spin continuously spins the view around.

  • Rock continuously rocks the view left-to-right.

  • Zoom in/out slightly zooms in/out the view. Convenient buttons for touchscreens.

  • Tilt Lock can be toggled using Ctrl + b keyboard shortcut. In tilt lock mode 3D view rotation is restricted to the azimuth axis (left-right direction) by disabling rotation around elevation axis (up-down direction).

Slice View

Three default slice views are provided (with Red, Yellow and Green colored bars) in which Axial, Saggital, Coronal or Oblique 2D slices of volume images can be displayed. Additional generic slice views have a grey colored bar and an identifying number in their upper left corner.

Slice View Controls: The colored bar across any slice view shows a pushpin icon on its left (Show view controls). When the mouse rolls over this icon, a panel for configuring the slice view is displayed. The panel is hidden when the mouse moves away. For persistent display of this panel, just click the pushpin icon. For more options, click the double-arrow icon (Show all options).

View Controllers module provides an alternate way of displaying these controllers in the Module Panel.

  • Reset field of view (small square) centers the slice on the current background volume

  • Show in 3D “eye” button in the top row can show the current slice in 3D views. Drop-down menu of the button contains advanced options to customize how this slice is rendered: “…match volume” means that the properties are taken from the full volume, while “…match 2D” means that the properties are copied from the current slice view (for example, copies zoom and pan position). Typically these differences are subtle and the settings can be left at default.

  • Slice orientation displays allows you to choose the orientation for this slice view.

  • Lightbox to select a mosiac (a.k.a. contact sheet) view. Not all operations work in this mode and it may be removed in the future.

  • Reformat allows interactive manipulation of the slice orientation.

  • Slice offset slider allows slicing through the volume. Step size is set to the background volume’s spacing by default but can be modified by clicking on “Spacing and field of view” button.

  • Blending mode specifies how foreground and background layers are mixed.

  • Spacing and field of view Spacing defines the increment for the slice offset slider. Field of view sets the zoom level for the slice.

  • Rotate to volume plane changes the orientation of the slice to match the closest acquisition orientation of the displayed volume.

  • Orientation Marker controls display of human, cube, etc in lower right corner.

  • Ruler controls display of ruler in slice view.

  • View link button synchronizes properties (which volumes are displayed, zoom factor, position of parallel views, opacities, etc.) between all slice views in the same view group. Long-click on the button exposes hot-linked option, which controls when properties are synchronized (immediately or when the mouse button is released).

  • Layer visibility “eye” buttons and Layer opacity spinboxes control visibility of segmentations and volumes in the slice view.

  • Foreground volume opacity slider allows fading between foreground and background volumes.

  • Interpolation allows displaying voxel values without interpolation. Recommended to keep interpolation enabled, and only disable it for testing and troubleshooting.

  • Node selectors are used to choose which background, foreground, and labelmap volumes and segmentations to display in this slice view. Note: multiple segmentations can be displayed in a slice view, but slice view controls only allow adjusting visibility of the currently selected segmentation node.

Mouse & Keyboard Shortcuts

Generic shortcuts

Shortcut Operation
Ctrl + f find module by name (hit Enter to select)
Ctrl + o add data from file
Ctrl + s save data to files
Ctrl + w close scene
Ctrl + 0 show Error Log
Ctrl + 1 show Application Help
Ctrl + 2 show Application Settings
Ctrl + 3 show/hide Python Interactor
Ctrl + 4 show Extensions Manager
Ctrl + 5 show/hide Module Panel
Ctrl + h open default startup module (configurable in Application Settings)

Slice views

The following shortcuts are available when a slice view is active. To activate a view, click inside the view: if you do not want to change anything in the view, just activate it then do right-click without moving the mouse. Note that simply hovering over the mouse over a slice view will not activate the view.

Shortcut Operation
right-click + drag up/down zoom image in/out
Ctrl + mouse wheel zoom image in/out
middle-click + drag pan (translate) view
Shift + left-click + drag pan (translate) view
left arrow / right arrow move to previous/next slice
b / f move to previous/next slice
Shift + mouse move move crosshair in all views
Ctrl + Alt + left-click + drag rotate slice intersection of other views (Slice intersections must be enabled in Crosshair selection toolbar)
v toggle slice visibility in 3D view
r reset zoom and pan to default
g toggle segmentation or labelmap volume
t toggle foreground volume visibility
[ / ] use previous/next volume as background
{ / } use previous/next volume as foreeround

3D views

The following shortcuts are available when a 3D view is active. To activate a view, click inside the view: if you do not want to change anything in the view, just activate it then do right-click without moving the mouse. Note that simply hovering over the mouse over a slice view will not activate the view.

Shortcut Operation
Shift + mouse move move crosshair in all views
left-click + drag rotate view
left arrow / right arrow rotate view
up arrow / down arrow rotate view
End or Keypad 1 rotate to view from anterior
Shift + End or Shift + Keypad 1 rotate to view from posterior
Page Down or Keypad 3 rotate to view from left side
Shift + Page Down or Shift + Keypad 3 rotate to view from right side
Home or Keypad 7 rotate to view from superior
Shift + Home or Shift + Keypad 7 rotate to view from inferior
right-click + drag up/down zoom view in/out
Ctrl + mouse wheel zoom view in/out
Ctrl + b toggle tilt lock
+ / - zoom view in/out
middle-click + drag pan (translate) view
Shift + left-click + drag pan (translate) view
Shift + left arrow / Shift + right arrow pan (translate) view
Shift + up arrow / Shift + down arrow pan (translate) view
Shift + Keypad 2 / Shift + Keypad 4 pan (translate) view
Shift + Keypad 6 / Shift + Keypad 8 pan (translate) view
Keypad 0 or Insert reset zoom and pan, rotate to nearest standard view

Note: Simulation if shortcuts not available on your device:

  • One-button mouse: instead of right-click do Ctrl + click

  • Trackpad: instead of right-click do two-finger click