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The Viewers and Colormap Editor

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Orthogonal Viewer Control

The Orthogonal Viewer consists of essentially two parts, the viewer window (shown as A in Figure 2) and the viewer controls (B--H in Figure 2). The Viewer is capable of displaying different combinations of views as detailed in the display modes table below. The mouse can be used to pan/zoom the display as described in the Navigating the Display section below.

The controls (B--H in Figure 2) have the following functionality:

2. The mode selectors. The drop menu "3-Slice Mode" is the Main Display mode control. The viewer can be switched from either a number of "2D" modes e.g. the 3-Slice Mode shown, to a 3D mode to combinations of 2D and 3D Modes. See the display modes table below for all the options. The drop menu "3-slice" mode is the 3D Mode Selector. This determines what is displayed in the 3D view (if it appears). These options include "none", orthogonal-"card" views, volume renderings, oblique slices and combinations of the above. The final drop menu "box" determines whether a box, or the coordinate axis are displayed in the 3D view.
3. The two buttons marked "Volume" and "Oblique" bring up the Volume Rendering and Oblique Controls which control how volume renderings and oblique slices are displayed. See below for more detailed explanations.
4. This is the coordinates frame, which can be used to display Talairach coordinates in neuroimaging applications. In the specific example the viewer cross-hairs are on the AC which has image coordinates 87,90,64 but Talairach coordinates 0,0,0 as shown in the black textbox -- see the Coordinates page for more details. The three checkboxes
1. "x-hairs" -- disables the viewer changing positions when the left mouse button is clicked in the viewer. This viewer essentially locks/unlocks the viewer.
2. "Lb" -- this turns on/off the label/axis display in the viewer
3. "Interp" -- this turns on/off Open GL blending interpolation of the image. If this is off and the image is zoomed sufficiently then individual voxels can be seen!
4. "T-Grid" -- This option to overlay a Talairach grid on top of an anatomical is only available in the 3D view.  This option is described in the Coordinate Systems manual page.
5. Frame E is the image navigation frame where the user can set the X, Y and Z coordinates. These coordinates are in image space, i.e. Z=slice number, and X and Y are the in-plane voxel coordinates. The main panel (E1) is the set of controls for the regular orthogonal viewer. The objectmap orthogonal viewer has one additional control (See E2), titled mask which controls the transparency of the objectmap (0=completely transparent, 100=completely opaque). The 4D Viewer has two additional controls (See D3). These are the Frame scale (which also appears in the other viewers if the image is four-dimensional, i.e. 3D + time), and the Movie Control button which brings up the movie control for displaying cine-loops of the 4D image.
6. This controls the image colormap. 
1. St -- this uses a standard colormap where the minimum image intensity is mapped to black and the maximum to white with liner interpolation between them. This often gives bad contrast for MRIs.
2. Nr -- this colormap -- which is the default -- is set to automatically "window" the image to saturate the image at the 99% of its cumulative histogram. This has been empirically shown to improve the contrast of MRI images
3. F1, F2, F4 are overlay colormaps used by the Overlay Control to display merged functional/anatomical images. See the Registration page for more details.
4. Cmap -- this brings up the Colormap Editor, described in more detail below, which can be used to create/edit custom colormaps.
7. The zoom buttons can be used to zoom in/out simultaneously in all views of the orthogonal viewer. (Individual slices can be zoomed in/out using the middle mouse button).  The Reset button can be used to reset the display to a default orientation -- this is useful in 3D views when the image has been placed in a "bad angle". Finally the Save button can be used to grab a screen-shot of the viewer frame (A) and save it to either a JPEG (if the extension .jpeg or .jpg is specified) or a TIFF file otherwise. If the image is 4D, a screen-shot for each frame can be saved using the SaveAll button -- see Frame G2.
8. The little "x" button can be used to hide the controls to maximize display area for the viewer. Clicking it back restores the controls.

Auxiliary Controls

There are five auxiliary controls which may be available, and which which have been referenced above, namely:

1. The Volume Control
2. The Oblique Slice Control
3. The 3D Renderer Controls
4. The Movie Controls
5. The Colormap Editor

Navigating in the Display

The images are displayed in the black area on the left side of the viewer window. There are a variety of ways to manipulate the views and move through them. For the most efficient control, the use of a three-button mouse is recommended.

Mouse Control in the viewing area

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Button 1 (left)

Click the left mouse button (button 1) anywhere on any of the 2-D slice views to set the cross-hairs to this point. Click and hold button 1 as you drag through the view space to move the cross-hairs cursor when it is active, and to rotate the 3-D display, when it is shown. (Unchecking the "x-hairs" box in the viewer control panel disables mouse-in-viewer movement of the cross-hairs. In this case, use the slider bars as described below.)

Button 2 (middle/wheel)

Click and drag with button 2 to scale the display. Drag down to zoom in, and drag up to zoom out.

Button 3 (right)

Clicking and dragging with mouse button 3 translates the display. Use it to slide the display up, down, and side to side. Pressing the shift key and the right mouse button brings up the Renderer Control.

The axes

The axis display is based on the image's native directions (usually X and Y are in the plane of the slices, and Z is across the slices). In the viewer, the X-axis is red, the Y-axis is green, and the Z-axis is blue.

Navigation controls in the viewer control panel

Available Display Modes

The Main Display Mode Selector		The 3D Mode Selector
3-Slice mode The default display mode is "3-Slice mode," which shows three two-dimensional views of the image; an axial slice, a coronal slice, and a sagital slice, arranged to maximize available display space.		3-Slice Show the three 2-D slices in their relative orthogonal orientation
3-Slice+3D Mode This mode gives the three 2-D displays as in the default, but adds a large three-dimensional viewing space in the bottom right corner. This three dimensional view has multiple options, which can be accessed by the leftmost second-row menubutton in the viewer control panel		None Do not display any image in the 3-D area
Simple mode This display mode shows all three two-dimensional sections as in 3-Slice mode, but arranges them side-by-side.		Volume Display a full volume rendering of the image
3-Slice+3D Mode(2) This view mode is the same as the "3-Slice+3D Mode," except the four view spaces are allocated equal display space.		Obl+Vol Show the volume with the oblique slice through it
Obl+3-s Show the 3-slice rendering, along with a fourth oblique slice		3-s+vol Show the full volume rendering, as well as the positions of the three slices, corresponding to the other three views.
3-s+vol+o Show all three views as describe above, overlaid simultaneously		Sagittal-YZ This shows only the 2-D view in the YZ plane
Coronal-XZ Shows only the 2-D view in the XZ plane		Axial-XY Shows only the 2-D view in the XY plane
3D Only Fills viewer area with the 3-dimensional view, as described in "3-Slice+3D Mode"		Oblique Show a slice through the image in any orientation

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Volume Control

Clicking the Volume button in the third row of the viewer control panel (See Figure 2C) brings up the Volume Control Dialog box. This lets you set the display properties for the volume rendering of the image if it is shown.

There are two volume rendering methods used, a hardware accelerated (2D) Texture mapping method or a software ray-casting method. If the Texture Map checkbutton is enabled the Texture Mapping method is used. The ray casting method can yield higher quality displays, but it is much slower if a decent graphics card is available. The Resolution of the volume is controlled using the drop-menu labeled "Half-Original", just below the texture map button. Setting this value too high will place a large computational burden on the system. The image needs to be resampled prior to display, the interpolation mode for this is controlled using the drop menu marked "linear". Shading may be enabled using the Shading button.

The "Cropping" tools let you crop the image in all three dimensions, from either the max or min direction (or both). The sliders on the right side will, by default, be at the maximum value in their respective dimension. This is a quick check of the dimensions of your image.

The St Nr F1 F2 and F3 buttons at the bottom of the Volume Control Dialog box are some pre-set colormap options. If these are insufficient, clicking the Colormap button brings up the Colormap Editor, allowing you to create your own color scheme, or select from a wider variety of presets. See below. This is a separate colormap editor from that used for slice display (See Figure 2F).

The "Show Volume" checkbox sets whether the 3-D volume rendering should be displayed at all.

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Oblique Control

Clicking the Oblique button in the third row of the viewer control panel (See Figure 2C) brings up the Oblique Control Dialog box. This lets the user manipulate the oblique slice, used to display non-orthogonal views of the current image.
This can either be positioned manually or automatically. For manual positioning, the user needs to adjust (i) the normal of the plane using the x-norm, y-norm and z-norm sliders and (ii) the offset of the plane centroid using the Distance slider. The Reset button is used to place the oblique slice in its default

"Automatic" positioning works by placing the slice perpendicular to the current viewer angle, this is enabled/disabled using the Follow Camera checkbox, which adjusts the plane in real time to follow the viewer camera. Alternatively the Look to Camera button may be used to perform this once. The Edge Camera button places the slice at the front of the camera clipping range (see the Renderer Controls for an explanation.) axial position.

The image display is controlled by (i) the main colormap – this is the same as for the main viewer (see Figure 2F), (ii) the resolution at which the slice samples the underlying image (this is set by the Res: drop menu – 256x256 is the default), and (iii) the opacity which can make the oblique slice more or less transparent – this is controlled by the Opacity slider.

There area also a number of miscellaneous controls.

The Show button enables/disables the display of the oblique slice. The Normal button shows/hides the normal direction arrow. The Load Plane and Save Plane buttons can be used to save the position and orientation of the current oblique slice in a text file for later retrieval. Finally the Save Image button can be used to save a 2D image of the current texture mapped on the oblique slice.

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The 3D Renderer Control

3D Rendering techniques employ the formalism of a 3D scene being viewed by a camera positioned somewhere in the scene – the actual screen display is what the "camera" sees in the 3D scene. Manipulating the position and orientation of the camera can produce very different views.

While all viewers in BioImage Suite are true 3D viewers and employ 3D rendering techniques, when displaying a two image the user can only move the camera in very restricted ways – parallel to the image plane being displayed and can not change its orientation.

When part (or the whole of) the Orthogonal Viewer is set to 3D Mode, the user can explicitly rotate the volume etc. using the left mouse button. This moves the camera that generates the 3D Rendering. Pressing Shift+Right Mouse button in the 3D viewer brings up the 3D Renderer Controls which can be used to perform additional camera operations. In particular they can be used to move the camera to preset positions using the View drop-menu (currently displaying "Axial-XY"). A current position can be stored as a preset using the Add button and the current preset updated from the current camera position using the Upd button. All Camera position presets maybe loaded and saved using the Load and Save buttons respectively.

The two sliders Near Plane and Thickness control the camera clipping, and restrict the 3D rendering to display only objects that are in a range of distances perpendicular to the camera. The Rt button on the far right resets the clipping range to show all objects in the scene (e.g. image volumes, slices, surfaces etc.).

The top row contains controls to Zoom the camera (Zm), the reset to the original orientations (XY,Cl) and to save the scene to a jpeg/tiff file as described earlier (see Figure 2 and it's description).

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The Movie Controls

The movie control is accessed using the "Movie Control" button in the 4D Orthogonal Viewer -- See Figure 2 E3). It has functionality for playing cine-loops of the contents of the viewer. It has two distinct play modes "Complete" which is equivalent to simply incrementing the frame and "Fast" which uses cached versions all frames prior to playing to achieve higher performance at the loss of interaction during movie mode. The caching is performed by clicking the "Prepare" button.

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Mosaic Viewer Controls

The simple viewer, or "Mosaic Viewer" displays multiple 2-dimensional slices, simulating common radiology and MR figures. You can pull an image from the orthogonal viewer into the mosaic viewer in order to quickly compare multiple slices at once, or visualize it in standard ascending/descending slice order.

Manipulating the Slice Views

Once an image has been loaded into the mosaic viewer, you can change a number of options regarding how it is displayed.

Slice Orientation

From the menu at the top of the viewer control panel you can choose the direction in which the slices will move through the image. Choose "Axial-XZ" to have the viewers display slices from top to bottom, "Sagittal-YZ" to have them display slices in profile, and "Coronal-XY" to display slices from front to back.

Number of Viewers

Sliding the button on the "Num Viewers" slider bar, will adjust the number of individual viewer panels in the display space. The size of the viewers is adjusted automatically so that they all fit in the display. Adding viewers allows you to see more slices at once but allocates less display space for each slice.

First Slice

Use the "First Slice" slider bar to select which slice will be displayed in the top left viewer. This will set the lowest slice displayed. Use it in combination with the Increment slider to maximize the usage of the display, and show the most interesting parts of your image in the highest slice density.

Increment

The "Increment" slider sets the number of slices to skip between successive viewers in the 2-D display. Thus, the display starts with the slice specified by the "First Slice" slider, and adds every nth slice to each following viewer in order, where n is the increment selected. If a large increment is selected, there may not be enough slices to fill all viewers, leaving those near the end blank. If a small increment is selected, consecutive slices will be very close together, and the viewers may fill up with slices within a short distance from the first slice.

Labels and Interpolation

The checkboxes for labels and interpolation turn the label display in each viewer on and off, and the display interpolation between voxels on and off, respectively.

Colormaps

The standard and custom colormaps can be applied to the 2-D displays just as for the orthogonal displays as described below.

Zoom

Clicking the arrows on either side of the Zoom label will zoom all viewers to the same level. To zoom an individual viewer's display, click and drag on it with the middle mouse button. (Clicking and dragging with the right mouse button will pan the display). These changes can be reversed by hitting the Reset button.

Save

Click the Save button to save the whole mosaic display as either a JPEG or TIFF image.

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Using Colormaps

Accessing the Colormap for an Image

(Note: an image must be loaded to access the colormap editor). Once an image has been loaded into the viewer, you can simply click on the Cmap button on the lower right side of the viewer control panel. This will bring up the colormap editor window. (Fig. 4)

Colormap Settings

The default linear relationship is appropriate for many applications, but you may want to customize the colormap for you image. The simple controls to do this are in the main colormap window (Fig. 3). Use the menu right under the colormap function display to select which type of function you want to use to define your color map. You can also use the Complex Controls.

Step

Gamma

Complex Colormap Controls

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