Why VivoQuant? VQ features Plugin Modules Download VQ!


Main window, menus and docks

Main window

Upon opening VivoQuant, the VQ main window appears. The main window contains the primary VQ display and also serves as the main access point for reaching all other VQ functions.

Menus and thumbnails icons

Used for file manipulation and includes options for opening, saving, printing and publishing files. Also used to control the display of data already loaded into VivoQuant. Researchers can toggle between different datasets and have  a variety of display options, including layout and zoom. The tools menu provides access to several image processing tools, including data control, reconstruction, calibration and configuration features. A bank of thumbnail icons is located below the menus.


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. Multiple controllers are dockable at any given time.

Views and display functions

Patient names, position labels, slice number and layout

Patient name/labels are displayed on the bottom of all images (sagittal, coronal and transversal) and also on the MIP. The position labels indicate which side of the mouse is being viewed: plane of view, (i.e. sagittal, coronal and transversal), the left/right side and anterior/posterior side. The slice number is useful to compare the same slice of an object at different time points. The layout offers a variety of viewing: all slices can be viewed simultaneously with the MIP in a 2×2 or 1×4 grid or the user can view just the slices with the option of focusing in on the transversal view.

Cross-hairs, palette and zoom

The cross-hairs function is displayed over each cross-sectional image (sagittal, transversal and coronal). The different slice views are synchronized, with the cross hair showing the current position in all slices. The palette field is used to select a color scheme and thresholding for the displayed data sets. A large list of available color maps are available. The zoom function enhances viewing and allows you to alter the viewpoint of the image by panning in and out or going to a full screen view.

MIP: Maximum Intensity Projection view

A Maximum Intensity Projection (MIP) is a series of 2D images generated from a 3D reconstruction. It selects the maximum value through the reconstruction “seen” by each 2D pixel at each of several viewing angles. Each angular view in a MIP has a unique viewing angle which defines the 2D projection plane. Repeating this process for multiple angles around the animal generates what appears to be a “rotating film” of the reconstructed image.

Multi-Planar Reconstruction (MPR)

Simultaneously displays a sagittal, coronal and transversal slice of the reconstruction, which freely rotates and is zoomable in 3D.

Tile view and time series

The tile view displays an array of slices. The time series is available from the tile view and allows the operator an easy way to visualize sets of dynamic data.

Invicro 3D-ROI (Region of Interest) tool
Manual segmentation, semi-automated segmentation, full automated segmentation

The 3D ROI operator provides advanced tools for drawing, visualizing, saving and quantifying both 2- and 3-dimensional regions. The acronym “ROI” stands for “region of interest” and is used to describe a particular area or volume within an image for which the user wishes to characterize some quantity or quality.

Manual segmentation: “painting in 3D”

Painting mode uses a circle or 3D-sphere tool to classify voxels in one of the three orthogonal views. The spline tool allows users to draw and manipulate ROI shapes, as well as to add or remove regions in free hand mode or with the thresholding tool. Any ROI can easily be eroded or dilated to remove or add to the outer layer of voxels. This feature is useful to fine-tune and clean up images, as well as to compensate for partial volume effects or images with limited resolution.

Semi-automated segmentation

The 3D ROI tool provides powerful thresholding methods. The “Global Thresholding” classifies all voxels within a given value range. The “Connected Thresholding” allows users to set a seed point, from which all voxels in the given range are added to the ROI. This would allow easy segmentation of lungs or Xenograft tumors, for instance. Many more thresholding types are available.


Automated segmentation: “histogram”

Automatic segmentation can be achieved through different ways. Histogram-based auto-thresholding allows users to separate any input ROI into the foreground and background regions. The histogram tool analyzes the values in each ROI individually, showing the frequency and distribution of values. Confidence-connected auto-thresholding evaluates voxels in the area and adds voxels within a certain variance- and mean-based confidence level (with a seed point).

Quantification, specific activity and specific value uptake calculator

The quantification tool provides a means to quantify density and activity parameters in CT and NM, MR, PET, or SPECT images, respectively. The tool provides several options for generating quantification data. There are multiple methods for setting the region of interest, flexibility in selection of the quantification view direction, easy-to-read presentation of data found in the quantification table and options for saving and loading ROIs or plotting data.


As a first step an ROI around an organ or tumor needs to be drawn. Four ROI types are available: Spline, Freehand, Bully and Isocount. Once the desired ROI has been defined, the quantification table will display a wide range of information, such as volume, sum, concentration, unit, standard deviation, etc.

QuantiCal, specific activity calculator and specific uptake value calculator

Biodistribution visualization

The biodistribution visualization tool creates an atlas representation of measured mouse biodistribution values.

Reorientation/registration tool

The reorientation/registration tool enables manual and automatic realignment of image data via translation, rotation or flipping. Reference and input data may be manipulated separately. Specific translation settings may be saved or loaded for future studies. There is also an option for setting automatically applied default image shifts.

Distance measure, cropping, arithmetic, checker board and filtering tools

Distance/annotation tool

The distance/annotation tool enables you to measure the distance between two points in any image. For example, it can be used to measure the size of a tumor by measuring its length, depth and width. One of the most powerful options available with the distance measure is the capability to perform landmark co-registration. The images can be annotated with appropriate description labels and arrows or rulers pointing to specific organs of interest. 


In checkerboard mode, the reference and input data set(s) are arrayed in a pattern of alternating squares, resembling a checkerboard. This mode is especially useful when checking image registration.


The cropping tool allows images to be cropped to highlight their important features, removing any unnecessary or unwanted areas. For instance, it can be used to remove empty spaces around the animal or to extract just the skull in preparation for further brain image-processing.

Arithmetic tool

The arithmetic tool can be used to add, subtract, multiply, divide, average or merge multiple images.

Filtering tool

The filtering tool offers a variety of smoothing filters.

3D volume rendering and Image Magick suite

3D volume rendered

VivoQuant offers full 3D volume rendering, a powerful visualization tool, for all data sets. Transfer maps showing gradient and intensity allow users to set individual opacity values.

The Image Magick options provide an excellent tool for generating informative movies for dynamic and gated data acquisitions. These tools allow the user to combine data sets in meaningful ways to reflect the dynamic nature of the physiological processes taking place.

Split movie into frames

This option takes a movie (options include .gif, mpg, .mng and .mpeg) and splits it into individual frames.

Join frames to movie

This tool provides the opposite function of the previous tool, allowing the user to take individual images (options include .png, .bmp, .jpeg, .jpg and .tif) and combine them into a movie (options include .gif, .mng,.mpg, and .mpeg).

Change delay

Depending upon the size and style of movie made, the default frame time may be too fast or too slow. This tools allows the user to select a pre-existing movie and change the frame time (given in milliseconds).

Image to poster

The ImageMagick suite enables the creation of high-quality images–the kind of images often used at
conferences and in presentations. To help facilitate the f use of such images, this option automatically allows the user to place an image into a poster.

Image to capture

The image-to-capture feature allows an image or movie to be loaded from a file on the local machine, edited and then re-saved. The capture viewer also supports importation of the image/movie into a DICOM/iPACS repository.

CT tools

Several CT tools are available, such as bed removal, resampling data and CT windows preset.

Min/max tool

The min/max tool allows you to see and adjust the minimum and maximum values of all loaded studies.


The DICOM Study Browser displays the DICOM data found in the selected repository. Filter, Show Data Type and Find options can be used to limit the data displayed in the Study Browser. As a DICOM database grows, the filter tool becomes useful for sifting through studies. Options for filtering include Patient’s Name, Patient’s ID, Study Description and Study Date. Users can make additions and editions to the DICOM repositories. These repositories can be local folders containing DICOM files or DICOM network servers (iPACS)  located on a local or remote computer. The DICOM dump tool provides the information contained in the DICOM headers for a DICOM file currently loaded. Many others DICOM tools are available.

Optional Atlas plugins NM/CT and fMRI

Optional automated Tumor Segmentation and Data Processing Modules for fMRI and NM/CT analysis. Read more about Invicro atlases

High Throughput modules

Preprocessing Tool

The Preprocessing Tool allows users to prepare image data sets for analysis.


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