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Visualization Configuration

In the visualization Configuration, you can visualize images, meshes and fibers in single view or multiple views. For both, images and meshes, the visualization attributes can be modified.

The Visualization configuration consists of :

    • Database Access Column: It is used to retrieve data from database. Just select the patient name and then drag and drop the desired data into the visualization area.
    • Visualization Area: It is used to visualize the data, it can have one or multiple views.
    • Tabbing Button: It is used to open multiple visualization area tabs.
    • View Properties Toolbox: It has several tools that allow to control the visualization attributes like zooming, position, transfer function, and rendering modes.
    • Layout Toolbox : It is used to change the Visualization Area layout, allowing either single, multiple or custom distributed views.


Layout toolbox

This toolbox controls the number of views and its distribution in the visualization area. The three possible layout modes are:

    • Single Mode. There is only one single view in the visualization area, still several data can be dragged and dropped, layered and displayed one on top of the other.
    • Mutli Mode. There is a new view generated every time data is dragged and dropped into the visualization area. The visualization area will be equally split in order to show simultaneously every view. In this mode there will be one single view per data.
    • Custom Mode. The visualization area can be split either horizontally, vertically, one big view at the right side and two (or three) other smaller at the left, three orthogonal views and one 3D or up to 5x5 equally distributed matrix of views, as shown in the image. Every view can still have several data layered.


 View Properties toolbox

The view properties toolbox allows you to adjust the attributes that control the images and meshes visualization. This toolbox is divided in three areas.


(1)Static Area: It has two check-boxes to display the Scalar Bar and Annotations in the current view. This area is visible whether the displayed view is 2D or 3D.

(2) Layering Area: This area shows the properties of each data layered with their corresponding values.

When the layout mode is Single or Multi, an image or a mesh is dragged and dropped in the visualization area, this data will be layered automatically by medInria. To see the layered data information (e.g. patient name) you should wait when the cursor is on that layer.

Each layer can be individually selected by clicking on it and its respective visualization properties will be shown and could modified. Every image added has a corresponding layer number and the corresponding properties (shown in the image) that can be modified are the visibility, the opacity, the predefined Look-up tables that map scalar values of the layer into colour and the transfer function predefined window/level values.


The mesh layers are denoted with the string "Mesh". They also can be individually selected and its respective visibility, opacity, Edge Visibility, Color, and mesh rendering type can be modified.


 (3) Dynamic Area: This area changes depending on the view type displayed, 2D or 3D. The values that can be modified when the view is displayed in 2D are:

    • Axis. That are placed at the current position selected.
    • Windowing. Contrast/Brightness. Control the window/level values of the look-up table.
    • Slicing. I used to select a voxel from the view.
    • Zooming. Is used to zoom in/out the image.
    • Measuring. That activates you the measure in milliliters between two selected points.
    • Ruler. An horizontal and vertical 82 millimiter ruler.

When the user changes the type of the view from 2D to 3D, the dynamic area in the view properties toolbox change as shown in the image:


 The values that can be modified when the view is displayed in 3D are:

    • 3D Mode. Selects in between a composite Volume Rendering, Maximun Intensity Volume Rendering, Minimum Intensity Volume Rendering or 3D multi-planar view.
    • Renderer. Selects from the a volume rendering type
    • Cropping. It can be used to select only a part of the whole image to display in 3D

The view and its controls

The view is where the data is display either in 2D or 3D, there can be several views inside the visualization area and several data can be contained and displayed in the view

Annotations in the view

When the view is display in 2D the four anatomical directions (out of Left, Right, Posterior, Anterior, Superior, Inferior) are indicated by its initial letters displayed in the middle of each image border. Also important information obtained from the data file is displayed in the view corners.

    • In the Top Left corner you can find: The image size in voxels, the voxel size in millimeters both along the x and y direction. The x and y voxel coordinates of the currently selected voxel and its intensity value. The x and y position of the currently selected voxel in millimeters with respect to the world coordinates system. And the window/level values that control the transfer function.
    • In the Bottom Left corner you can find: The currently zooming percentage. The currently selected slice and the total number of slices along the z direction. And the voxel position along z axis with respect to the world coordinate system.
    • In the Top Right corner you can find: The name of the patient, the name of the study and the name of the file.
    • In the Bottom Right you can find the currently displayed view plane.


When the view is displayed in 3D the initial letters of the patient relative directions are shown in a cube in the left corner. In the top right corner you can find the name of the patient, the name of the study and the name of the file.

The annotations can be switch on/off with the check-box in the View Properties Toolbox.

View's toolbar

The view has a toolbar made of:

    1. Play slices button. When active it scans through all the slices. Only works when the view is display in 2D.
    2. Slice slider. Indicated where the current slice is and can be use to go through the slices. Only works when the view is display in 2D.
    3. Position link button. It will synchronize zoom and position of selected views. If you have two or more views active in the visualization area, all the views that has the link Position button active will be displaying the same position at the same slice (or slices, if 3D Multi Planar Representation), being the current view changed the reference.
    4. Window/Level button. It will synchronize the window/level of the selected views. If you have 2 or more views active in the visualization area, all the views that has the link Window/Level button active will have the same window/level value, being the current view changed the reference..
    5. Full Screen button. To Put the view all over the visualization area.
    6. Close button. To close the view.


How to switch in between 2D viewing plane or 3D and controls

When the cursor is over a view you give one right button click on the mouse and select the desired 2D viewing plane (coronal, sagittal, axial) or 3D visualization type.


2D controls

While in a 2D view, the mouse interaction controls depend on what is chosen from the properties toolbox, been only one of the four possible options available at the time.

Zooming. By holding the left button pushed and moving the mouse up/down you can zooming in/out. By holding the middle button pushed and moving the mouse you can around . By scrolling with the middle button you can go through the slices.

Windowing. You set the window or level value by holding the left button pushed and moving the mouse. The window value will increase/decrease when you move the mouse to right/left, the level value will increase/decrease moving the mouse up/down.

Slicing. To use it you have to click left button is used to select a voxel pointed by the cursor. You can also scroll slices upward by holding the mouse left button pushed and moving the cursor up, or by scrolling up the middle button.

Measuring gadget. To use it you have to click on the view the first point appears and a second click will define the second point. By clicking and draging either of the points the measuring gadget can be redefined.

3D controls

While on the 3D viewing you can interact (rotate,pan, etc.) with objects in the view. To do the interaction you have to push and hold a mouse button and move the mouse, the interaction type depends on the button pushed and is proportional to the magnitude of the mouse motion; for example, small left-button motions cause small changes in the rotation of the objects around its center point. For a 3-button mouse, the interactions and respective button to push are:

    • Rotation. Move the mouse while pushing the left mouse button.
    • Panning. Move the mouse while pushing the shift+left mouse button (or middle button) 
    • Spinning. Move the mouse while pushing the ctrl + left mouse button. 
    • Zooming. Just scroll the middle button, no need to move the mouse.

4D controls 

Time Toolbox is embedded in the Visualization Configuration. Time toolbox is not there statically. However, when the user drags and drops a sequence, the time toolbox will appear in the visualization configuration dynamically.


In the image above, you can see the Time Management Toolbox. The user can play, step forward/backward and stop the sequence. Moreover, the user can change the speed of the sequence with the speed GUI items. The time related data for the seqence is written on the bottom of the toolbox. 

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