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3D Viewer: User FAQs

1,070 bytes added, 01:33, 22 October 2019
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== 1. Basic Usage ==
=== How to display a stack ===
* '''Channels:''' If displaying color images, this specifies the color channels which are to be displayed.
After clicking OK, the 3D object appears in the viewer window.[[#top|Top]]
To transform a specific object, that object needs to be selected. An object
is selected by a single left mouse click. Selection is indicated by a red
bounding box.[[#top|Top]]
# Select the corresponding object by clicking on it
# Click on -> Edit -> Attributes and select the attribute you want to change. [[#top|Top]]
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 powerpointpresentations.
To stop an animation, click on ->View->Stop animation. [[#top|Top]]
Note however, that this does not change the transformation of individual
3D objects. To reset them, too, select each object and click on
->Transformation->Reset transformation.[[#top|Top]]
->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]]
adjust the background color.
To use the current background color by default, see "[[#How to change general view settings"]].[[#top|Top]]
== 2. Surfaces ==
=== What is the idea of a surface ===
are assumed to belong to the object, values below are assumed to belong to
the background. To construct a surface, an algorithm like the marching cubes
algorithm can be utilized.[[#top|Top]]
=== How to change the color, transparency... of a surface ===
See "[[#How to change the color, transparency... of a 3D object"]]
=== How to change the isovalue of a surface ===
See "[[#How to change the color, transparency... of a 3D object"]]
You can also smooth all displayed surfaces by clicking on
->Edit->Smooth all surfaces[[#top|Top]]
The displayed surfaces can be exported to files in different surface file
formats. Currently supported is Wavefront (.obj) and Drawing Interchange Format
== 3. Volumes ==
=== What are volumes/volume renderings? ===
A volume rendering generates the 3D effect by putting the slices of a stack
one behind another, separated by a certain distance. To each pixel in each
slice a transparency value is assigned, which depends on the pixel's brightness.[[#top|Top]]
=== How to change the color, transparency, ... of a volume ===
See "[[#How to change the color, transparency... of a 3D object"]]
# Click on ->Edit->Fill selection to erase the volume which is covered
by the ROI. (Erasing means actually filling it with black).
== 4 Orthoslices: ==
=== What are orthoslices? ===
Orthoslices are three orthogonal slices through the volume. The three
slices show one xy-plane, one xz-plane and one yz-plane. [[#top|Top]]
=== How to change the color, transparency, ... of orthoslices ===
See [[#How to change the color, transparency... of a 3D object]]
=== 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 interactively
the position of each of the three slices.
There exist also keyboard shortcuts to adjust the slices: hold one of the
x, y, and z key pressed and use either the arrow keys or mouse scrolling to
adjust the slices.
To hide a slice, hold one of the x, y or z key pressed and hit the 'space' bar. [[#top|Top]]
=== How to hide a slice ===
See [[#How to change the displayed slice]]
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