You can also smooth all displayed surfaces by clicking on Edit › Smooth all surfaces Top How to export surfaces In order to smooth the surface of a 3D object, select the object and click on Edit › Smooth surface. See #How to change the color, transparency… of a 3D object How to smooth a surface See #How to change the color, transparency… of a 3D object How to change the isovalue of a surface Top How to change the color, transparency… of a surface To construct a surface, an algorithm like the marching cubes algorithm can be utilized. One common way to find a surface is to choose a threshold which divides object and background: Values above the threshold are assumed to belong to the object, values below are assumed to belong to the background. Intuitively, the surface of an object is understood as the border between the object and the background. Top Surfaces What is the idea of a surface To use the current background color by default, see #How to change general view settings. A dialog opens, which lets you interactively adjust the background color. To change the background color of the 3D world, click on View › Change background color. See #How to general view settings for how you can avoid to show local coordinate systems in general. There are two types of coordinate systems: One global coordinate system, which indicates the origin of the universe, and one local coordinate system for each object.įor hiding the global coordinate system, have a look at “How to general view settings”įor hiding the local coordinate system, select the object and click on Edit › Hide/Show and disable ‘Show coordinate system’. To reset them, too, select each object and click on Transformation › Reset transformation. Note however, that this does not change the transformation of individual 3D objects. You can reset the 3D universe to its initial view by clicking on View › Reset View. To stop an animation, click on View › Stop animation.
You can incorporate the resulting movie file in powerpoint presentations. If you want to include the recording in a presentation, save it via ImageJ’s ‘Save as AVI’ function.
The animation is now recorded for one full 360° rotation. If you now want to record such an animation, click on View › Start recording. The view begins immediately to rotate around the y-axis. To animate the view, click on View › Start animation. Top How to make animations and movie recordings Click on Edit › Attributes and select the attribute you want to change.
In greyscale images, this attribute has no effect. Channels: In color images, the channels attribute specifies the channels to be displayed.Otherwise, it specifies the lower threshold of displayed pixels. Threshold: In case of surfaces, the threshold specifies the isovalue of the surface.Transparency: The transparency of the 3D object: A value of 0 means fully transparent, a value of 1 means fully opaque.If ‘None’ is selected, the color is taken from the stack image. These attributes have the following meaning: Top How to change the color, transparency… of a 3D objectĬolor, transparency, threshold and displayed channels of color images are so-called attributes of 3D objects. Selection is indicated by a red bounding box. An object is selected by a single left mouse click. To transform a specific object, that object needs to be selected. Individual objects can be transformed with the same key/mouse combinations. On many platforms, it is alternatively possible to scroll (while the ‘Hand’ tool is selected) for zooming. Zooming: Zooming is done by selecting the ‘Glas’ tool in ImageJ’s tool bar and drag with the left mouse button.Translation: Dragging while pressing the ‘Shift’ key shifts the view.If no 3D object is selected, dragging with the left mouse button rotates the view around the universe center. Rotation: Select the ‘Hand’ tool in ImageJ’s tool bar.The user can rotate, translate and zoom in the 3D space: Two sorts of transformations are distinguished: 1. Top How to interact with the viewer (rotate, shift, zoom) Channels: If displaying color images, this specifies the color channels which are to be displayed.Īfter clicking OK, the 3D object appears in the viewer window.A value of 2 means here that the image is downsampled by a factor of 2 in x-, y- and z-direction. Resampling factor: Large images require downsampling before displaying, to be rendered interactively.For all other display modes, this value is the lower threshold of displayed values. Threshold: For surfaces, this is the isovalue of the surface.Display as: Stacks can be displayed as volume renderings, orthoslices, surfaces or surface plots.The user can select from a list of all open images. Image: The image which should be displayed in the viewer.A dialog window opens, asking for some information: After you have started the 3D viewer, click on File › Add content.