Main Window

Upon starting the VivoQuant, the VQ Main Window appears. The Main Window contains the primary VQ display and also serves as the focal point for reaching all other VQ functions.


Four Menus are arrayed across the top of the Main Window. These include:


Menu Function
File Used for file manipulation and includes options for opening, saving, printing, and publishing files.
View Used to control the display of data already loaded into the VQ. Entire data sets may be toggled as may a variety of display options, including layout and zoom.
Tools Provides access to several VQ image processing tools, including data control, reconstruction, calibration, and configuration features.
Help Help content, including registration information and the manual, are available in this menu.


The Viewer Control, MIP Control, Data Manager, and Operators are automatically placed into Docks upon opening. Docks may be dragged and dropped into and out of the Main Window display and multiple Controllers are dockable at any given time.


A bank of thumbnail icons is located below the Menus. These icons provide fast access to features.


Thumbnail Icon Function
Opens the Data Browser
Opens a browser that can be used to load Reference data.
Opens a browser that can be used to load Input data.
Opens the Save Image window.
Opens the Save Movie window.
Rearranges the data views into a 2 x 2 layout.
Rearranges the data views into a single row layout.
Changes the display layout to show only the sagittal, coronal, and transverse data slices but not the MIP.
Changes the display layout to show only the transverse data slices.
Zooms in 25%.
Zooms out 25%.
Opens the Viewer Control panel.
Opens the MIP Control Panel.
Opens the Data Manager Panel.

View Modes

Four viewing modes are available via a pull-down menu located next to the thumbnail icons.

View Mode Function
Slice View The Slice View (default) simultaneously displays images of single slices for the MIP, sagittal, coronal, and transversal views of the loaded data sets.
Tile View The Tile View displays an array of slices for either, sagittal, coronal, or transversal view of the loaded data sets.
Multi View The Multi View displays sagittal, coronal, or transversal slices of each data set adjacent to one another simultaneously.
MPR View The Multi Planar Reconstruction View simultaneously displays sagittal, coronal, and transversal slices in a single window.


The operators are available in a pull-down menu located next to the thumbnail icons.

Operator Function
Navigation Enables manually scrolling through the image slices and rotation of the Maximum intensity Projection (MIP).
inviCRO 3D ROIs Provides advanced tools for drawing, visualizing, saving, and quantifying both 2- and 3-dimensional regions.
Quantification++ Provides a mean to quantify density and activity parameters in CT and NM scans, respectively.
Reorientation/Registration Enables realignment of image data via translation, rotation, or flipping. In registration mode, a variety of registration algorithms are available to automatically register data from a wide variety of modalities.
Time Series Allows sagittal, coronal, and transverse slices of datasets from a time series to be played sequentially in a loop or easily scrolled through manually.
Distance Measure Allows you to measure the distance between two points in any image.
Checkerboard In checkerboard mode, the reference and input data set(s) are arrayed in a pattern of alternating squares, resembling a checkerboard.
Cropping Allows images to be made smaller by removing any unwanted areas.
Arithmetic Allows voxel-wise arimethic operations on two input images, or scalar operations on any number of input images.
Smoothing Uses a selection of built-in smoothing filters with configurable parameters.


The Display field comprises the principal component of the Main Window. All loaded data sets (up to 3) are visible in the Display field. Many tools and image-processing steps are visible as changes to the display of the data sets in the Display field. For instance, going to View/Crosshair will add/remove crosshairs to the data shown in the Display field.

Projections vs. Reconstructions

The Display window recognizes whether a loaded data set is projection data or reconstructed data. The default viewing scheme, known as Slice View, for reconstructed data (presented almost exclusively throughout this guide) includes a MIP and three separate viewing directions (sagittal, coronal, and transversal). When viewing projection data or sinograms (sets of CT projection data), the VQ displays the data accordingly. For example, transverse slices of projection data are displayed with a 'P' in the top-left corner to denote projection.

For CT data, selecting the correct layout, will display the relevant sinogram data. For the corresponding windows, the data are labeled as "sinogr.", denoting sinogram.

NOTE: It is not possible to view projection (non-volumetric) and reconstruction (volumetric) data simultaneously.


The Palette field is used to select a color scheme and thresholding for the displayed data sets. By right-clicking on a palette, a large list of available color maps appears. Click on one of the available color maps to change the color map for a particular data set. The slider bars can also be used to adjust the color thresholding for a given data set. For more details on color maps and color scaling, please see Color Maps and Color Scaling.