=== How to display a stack ===
After you have started the 3D viewer, click on '->File->Add content'. A
dialog window opens, asking for some information:
=== How to interact with the viewer (rotate, shift, zoom) ===
The user can rotate, translate and zoom in the 3D space: Two sorts of
trans- formations are distinguished:
==== 1. Transformation of the view: ====
;Rotation: Select the 'Hand' tool in ImageJ's tool bar. If no 3D object is selected, dragging with the left mouse button rotates the view around the universe center.
;Translation: Dragging while pressing the 'Shift' key shifts the view.
==== 2. Transformation of objects: ====
Individual objects can be transformed with the same key/mouse combinations.To transform a specific object, that object needs to be selected. An objectis selected by a single left mouse click. Selection is indicated by a redbounding box. [[#top|Top]]
=== How to change the color, transparency... of a 3D object ===
Color, transparency, threshold and displayed channels of color images areso-called attributes of 3D objects. These attributes have the followingmeaning:
* '''Color:''' The color of the 3D object. If 'None' is selected, the color is taken from the stack image.
* '''Transparency:''' The transparency of the 3D object: A value of 0 means fully transparent, a value of 1 means fully opaque.
The attributes can be changed by
# Select the corresponding object by clicking on it
# Click on -> Edit -> Attributes and select the attribute you want to change.
=== How to make animations and movie recordings ===
To animate the view, click on ->View->Start animation. The view beginsimmediately to rotate around the y-axis. If you now want to record such ananimation, click on ->View->Start recording. The animation is now recordedfor one full 360° rotation. The result is displayed in a stack.
If you want to include the recording in a presentation, save it via ImageJ's'Save as AVI' function. You can incorporate the resulting movie file in powerpoint presentations.
To stop an animation, click on ->View->Stop animation. [[#top|Top]]
=== How to reset the view ===
You can reset the 3D universe to its initial view by clicking on->View->Reset View. This resets the view.
Note however, that this does not change the transformation of individual3D objects. To reset them, too, select each object and click on->Transformation->Reset transformation. [[#top|Top]]
=== How to hide the coordinate system ===
There are two types of coordinate systems: One global coordinate system, whichindicates the origin of the universe, and one local coordinate system foreach object.
For hiding the global coordinate system, have a look at "How to general view settings"
For hiding the local coordinate system, select the object and click on->Edit->Hide/Show and disable 'Show coordinate system'.
See [[#How to general view settings]] for how you can avoid to show local coordinate systems in general. [[#top|Top]]
=== How to change the background color ===
To change the background color of the 3D world, click on->View->Change background color. A dialog opens, which lets you interactivelyadjust the background color.
To use the current background color by default, see [[#How to change general view settings]]. [[#top|Top]]
=== What is the idea of a surface ===
Intuitively, the surface of an object is understood as the border betweenthe object and the background. One common way to find a surface is to choosea threshold which divides object and background: Values above the thresholdare assumed to belong to the object, values below are assumed to belong tothe background. To construct a surface, an algorithm like the marching cubesalgorithm can be utilized. [[#top|Top]]
=== How to smooth a surface ===
In order to smooth the surface of a 3D object, select the object and click on->Edit->Smooth surface.
You can also smooth all displayed surfaces by clicking on->Edit->Smooth all surfaces [[#top|Top]]
=== How to export surfaces ===
The displayed surfaces can be exported to files in different surface fileformats. Currently supported is Wavefront (.obj) and Drawing Interchange Format(.dxf). [[#top|Top]]
=== What are volumes/volume renderings? ===
A volume rendering generates the 3D effect by putting the slices of a stackone behind another, separated by a certain distance. To each pixel in eachslice a transparency value is assigned, which depends on the pixel's brightness. [[#top|Top]]
=== How to edit volumes? ===
The 3D viewer offers the possibility to edit volumes. To crop volumes,
# Select an object by clicking on it.
# Use one of ImageJ's selection tools to draw a region of interest (ROI).
# Click on ->Edit->Fill selection to erase the volume which is coveredby the ROI. (Erasing means actually filling it with black).
=== What are orthoslices? ===
Orthoslices are three orthogonal slices through the volume. The threeslices show one xy-plane, one xz-plane and one yz-plane. [[#top|Top]]
=== How to change the displayed slice ===
The position of the three slices can be changed. To do so, click on-> Edit -> Adjust slices. A dialog opens, which lets you adjust interactivelythe position of each of the three slices.
There exist also keyboard shortcuts to adjust the slices: hold one of thex, y, and z key pressed and use either the arrow keys or mouse scrolling toadjust the slices.
To hide a slice, hold one of the x, y or z key pressed and hit the 'space' bar. [[#top|Top]]
=== What are surface plots? ===
A surface plot displays a 2D slice as a 3D plot: The x- and y-coordinatecorrespond to the x- and y-coordinate in the 2D slice, the z-coordinateis the pixel value at (x, y).
A 3D surface plot always shows one slice a time. When a 3D surface plotis opened in the viewer, the currently selected slice is displayed. Whenchanging the slice of the original image stack, the view is automaticallyupdated. [[#top|Top]]
=== How to change general view settings ===
Some general view settings can be changed and made permanent by clicking on ->View->View settings. A dialog window opens, asking the user for settings. There are two types ofsettings, startup options and options which are applied immediately.
# Startup options:
Now such a transformed object can be exported to a stack image again. To do so, click on ->Transformation->Export transformed image. The resulting stack image can of course also be saved via ImageJ's 'Save as' commands. [[#top|Top]]