After Slicer starts, two windows appear.

The Menu window provides menus for accessing the features of Slicer. A brief explanation of the Menu window will make it easier to refer to its parts later.

At the top of the Menu window there are File, View, Help, and Modules submenus.

Under the submenus is a group of buttons known as the Main menu.

Clicking a button on the Main menu will take you to the panel associated with that Slicer feature.

There are tabs along the top of each panel. The leftmost tab on each panel is the Help for that feature.

You can toggle a scrollbar on and off for the panel with this button.

Clicking More in the Menu window lists the modules available in your version of Slicer. Since Slicer consists of many optional modules, your list of modules may not match the list below.

Here are some sample modules:

  • Anatomy: saves files from a Slicer scene to use with the SPL Anatomy Browser.
  • Anno: controls the annotation displayed in the 2D and 3D viewer.
  • Colors: enables you to create your own color palette.
  • Custom: enables you to create your own modules for Slicer.
  • CustomCsys: lets developers add a Coordinate System actor to their module.
  • EMSegment: implements the "Expectation-Maximization-Segment" algorithm.
  • Endoscopic: places and controls a virtual endoscope in Slicer's scene, and presents the endoscope's view in a second window.
  • Fiducials: adds fiducial points on models in the 2D or 3D viewer windows.
  • Guidance: positions two spherical targets (red and yellow) in the 3D view window to support reformatting volumes.
  • Locator: connects Slicer to a server that feeds a real-time stream of coordinates from a device called the locator.
  • Measure: provides measuring tools to calculate Surface Area, Volume, and Cross Sectional Area.
  • MeasureVol: measures the volume of a segmented structure in a label map.
  • ModelCompare: shows point correspondences and models in 2D.
  • ModelHierarchy: displays the hierarchy of models.
  • Options: reorganizes the order of the modules and hides unnecessary modules.
  • Realtime: enables the locator's real-time coordinates to control Slicer.
  • SessionLog: records information about a segmentation session for Slicer development purposes.
  • Slices: selects the slices to display in the 3D viewer window.
  • Tester: allows the developer to test modules.
  • TetraMesh: reads in a Tetrahedral Mesh and converts it into a model.
  • View: customizes the size of the viewer window. The stereo mode allows viewing the 3D window in 3 dimensions, using red/blue glasses.
  • VolRend: selects the volume rendering method: Composite, MIP (Maximum Intensity Projection), or Isosurface.
  • VolumeMath: adds and subtracts volumes; finds the distance between two points in a volume.

The Viewer window (below) displays volumes and models.

In the Normal view mode, the upper part of the Viewer window is the 3D Viewer and the lower part is the 2D Viewer, for displaying 2D slices.