The basic organization of Slicer's user interface (UI) is shown above. This module's content will reference these following components, labeled in the figure: File Menu: Contains basic load and save functionality, access to application settings, Tcl and Python interfaces for developers, help and mechanisms for users to provide feedback. Toolbar: Contains tools for selecting and navigating among Slicer modules, layout and other utilities. GUI Panel: Contains a UI for any selected module. 3D Viewer: Displays a rendered 3D view of the scene along with some visual references to clarify its spatial orientation (A = anterior, P = posterior, R = right, L = left, S = superior and I = inferior).: 3D Viewer Controls: The blue bar across any 3D Viewer shows a pushpin icon on its left. When the mouse rolls over this icon, a panel for configuring the 3D Viewer is displayed. The panel is hidden when the mouse moves away. For persistent display of this panel, just click the pushpin icon. Slice Viewers: Three default slice viewers 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 Viewers have a grey colored bar and an identifying number in their upper left corner. Slice Viewer Controls: The colored bar across any Slice Viewer shows a pushpin icon on its left. When the mouse rolls over this icon, a panel for configuring one or all Slice Viewers is displayed. The panel is hidden when the mouse moves away. For persistent display of this panel, just click the pushpin icon. The Viewer Controller Module provides an alternate way of displaying these controllers in the main GUI panel.. Message Bar: Displays application messages and information.

Slicer contains a large and growing number of software modules which can be browsed and accessed in a number of ways. The image above shows the Module Navigation Tools in Slicer's Toolbar. The search icon allows keyword searching on all of Slicer's modules. The module's menubutton allows pull-down access to all of Slicer's modules, and the "history", "previous", and "next" icons allow recently visited modules to be easily re-selected.

Slicer's toolbar also contains quick links to core modules as shown in the image above (from left to right): Customizable "Home" Module The Applications Settings Interface (accessible from the File Menu: choose Edit->Application Settings) allows a Home Module to be specified for easy access from this icon. Models Module The Models Module provides information about models (polygonal datasets) and options for adjusting their display parameters. Transforms Module This module allows transforms to be created and edited. Data Module The Data Module displays the MRML scene tree, permits operations on the MRML tree, and creates and edits transformation hierarchies. The Load & Add Scenes or Datasets panel exposes options for loading many different data types. Helpful comments can be opened by clicking on the "information" icons next to each data type button. Volumes Module The Volumes Module provides information about volumetric datasets and provides options for adjusting display parameters. Tools for adjusting window and level are found here, for instance.. Annotations Module This module provides tools for creating and adjusting different types of annotation within the MRML scene. Annotations range from fiducial points, to ROI specifications to quantitative measurement tool like rulers at the present time. This module is currently under active development.s. Editor Module The Editor Module allows label maps to be created and edited. The module contains many manual and semi-automatic segmentation tools as well as options for Undo and Redo.