Table of Contents
3D Volume rendering plugin
User Manual
Introduction
The 3D volume rendering plugin allows the user to view and manipulate volume image data, such as MR and CT, in the three orthogonal planar views. The user can interactively select the plane coordinates of any of the orthogonal views.
Getting Started
To open a file using the 3D volume rendering plugin
- Open the Viewer Workspace.
- If in DualView mode, select the target Viewport (Left-mouse-click anywhere in the viewport in the data display area).
- In the Layer Controls, open the dropdown menu to the right of the Open File button.
- Select 3D volume(s). An open file dialog box appears. Navigate to and select the file(s) you want to open (multiple selection allowed using Shift+Left-mouse-click). Click Open. If successful, the opened 3D volume(s) will appear in the target viewport and layer GUI controls are added to the Layer Controls panel.
To open an object from the cart
- Open the Viewer Workspace.
- If in DualView mode, select the target Viewport (Left-mouse-click anywhere in the viewport in the data display area).
- Open the Cart Manager.
- Select the cart object(s) you want to open (multiple selection allowed using Shift+Left-mouse-click).
- In the Cart Manager, select the dropdown menu to the right of the Open button.
- Select 3D volume(s). If successful, the opened cart object(s) will appear in the target viewport and layer GUI controls are added to the Layer Controls panel.
File Formats supported
The 3D volume plugin was designed to support any of 3D volume formats that can be opened with
ImageJ. So far, the following file formats have been verified to open correctly:
- Analyze image
- NifTI image
- TIFF stack
- URLs with MIME type "image/analyze"
Cart objects supported
- derived classes of Volume3D
User interface
- GUI controls
- Show/Hide: button to show/hide the layer in the viewport
- Opacity: slider/spinner to adjust the opacity of the layer
- Image(s): slider/spinner to cine through multiple images of the current axis
- Contrast: slider/spinner to adjust the image contrast
- Brightness: slider/spinner to adjust the image brightness
- Axis: radiobutton group to select the current axis to view
- Flip: buttons to flip the images in the X,Y,and Z axes
- Expand/Collapse: button to expand/collapse the GUI controls
- Colormap: combobox to select colormap to apply to data
- Keyboard controls
- Left/Right Arrows: Previous/Next image
- Up/Down Arrows: Opacity Increase/Decrease
- HUD Thumbnails
- When a 3D Volume layer is selected, a heads-up-display (HUD) is overlayed in the viewport that shows the three orthogonal view thumbnails for the currently selected planes. Left-mouse-click and drag inside any of the orthogonal thumbnail views will change the currently selected plane to view.
- Status Bar: When the layer is selected, a status bar is displayed on the bottom of the viewport that shows:
- Name of the layer (top-left)
- Image dimensions of the current axis (top-right)
- Image coordinates relative to the bottom left corner of the current image (bottom-left)
- Current slice number for each dimension (bottom-right)
- Display scale
- When the layer is selected, the scale measurements in real physical dimensions are overlayed in the upper right hand corner of the current viewport.
Functional Specification
Data input methods
Serializing/deserializing
In the serialization process, following states are stored:
- Translation
- Rotation
- Scaling
- Opacity
- Brightness
- Contrast
- Active image index for each axis (Transverse, Sagittal, Horizontal)
Deserialization process restores values for all the above states.
Linking
- 3D Volume - 3D Volume: using the GUI controls, keyboard controls, and HUD thumbnail controls in the master layer will change all the corresponding controls in the slave layers.
- Image(s): slave layer is set to proportional image number of master layer (ie: if master layer image is set to 50 of 100 then slave layer is set to image 2 of 4)
- 3D Volume - 2D Image:
3D Volume - 3D Atlas:
- Opacity, Contrast, Brightness, Axis, Flip: mirrors master layer changes
- Image(s): slave layer is set to proportional image number of master layer (ie: if master layer image is set to 50 of 100 then slave layer is set to image 2 of 4)
Workspace Interoperability
None
Error Handling
| Method | Object | Error | Exception thrown | Notes |
|---|
load() | File | file not found | yes | java.io.FileNotFoundException |
| unrecognized or bad format | yes | java.util.zip.DataFormatException |
load() | Volume3D | URL syntax error | yes | java.net.MalformedURLException |
| URL not found | yes | java.net.UnknownHostException |
| URL connection error | yes | java.io.IOException |
| HTTP page not found | yes | java.io.IOException |
DarenLee? - 26 Apr 2009
