IJ Plugins: 3D Toolkit

Plugins
Clustering
Color
DCRaw
Image I/O
Half-Median
3D Toolkit
Example
Texture Synthesis
Libraries
ij-VTK
ImageJ-Zaurus
VTK Examples

	Caution
	This page is out of date, expecially regarding most curent versions of the plugins. `3D IO` and `3D Toolkit` moved to ij-plugins Toolkit bandle. `VTK Filters` moved to ij-VTK bandle.

3D Toolkit is a set of plugins for 3D and 2D operations on images in ImageJ. The toolkit has three groups of plugins:

3D IO - reading and writing of images in VTK and MetaImage formats.
3D Toolkit - native Java operations on 2D and 3D images.
VTK Filters - wrappers for VTK image filters.

3D IO

3D IO is a set of plugins reading and writing of images in VTK and MetaImage (ITK) format. All plugins in this set are scriptable using ImageJ macros.

3D Toolkit

Connected threshold region growing segmentation (example)
Auto volume clipping to a region that contains non-zero pixels
Morphological dilation (max)
Morphological erosion (min)

VTK Filters

A set of plugins that allow direct access to VTK image filters from ImageJ. All those filter will work on a single slice image when an image has multiple slices it is assumed that they form a volume (a 3D image). All filters can handle 8 bit, 16 bit, 32 bit integer or float pixel types. Here are some of the available filters, links in the brackets point to original VTK filter documentation:

Anisotropic diffusion - wrapper for VTK filter vtkImageAnisotropicDiffusion3D
Morphological dilation - wrapper for VTK filter vtkImageContinuousDilate3D
Morphological erosion - wrapper for VTK filter vtkImageContinuousErode3D
Gaussian smooth - wrapper for VTK filter vtkImageGaussianSmooth
Laplacian operator - wrapper for VTK filter vtkImageLaplacian
Median filter - wrapper for VTK filter vtkImageMedian3D

Use of vtk filter requires installed version of VTK with Java bindings. Filters were tested with VTK 4.2.

Installation

Follow the link and download latest ij-3D-Toolkit_bin_*.zip.
Locate your ImageJ plugins folder.
Remove from ImageJ plugins folder sub directories named '3D IO' and '3D Toolkit', if their exist.
Unzip content of ij-3D-Toolkit_bin_*.zip into ImageJ plugins folder
Add ij-plugins-tookit.jar to ImageJ class path. One of the ways to do it is by extending classpath in ImageJ startup script, for instance on Windows:
```
$ java -cp ij.jar;plugins/ij-plugins-toolkit.jar ij.ImageJ
```
On Unix like systems (including Linux and Mac OS X) the command would be almost the same:
```
$ java -cp ij.jar:plugins/ij-plugins-toolkit.jar ij.ImageJ
```
The only difference is that on Windows you use ';' to separate elements of a classpath, on Unix like systems you use ":". General information about installing ImageJ can found on the ImageJ installation page.
To use VTK filters add path to VTK Java classes typically located in vtk.jar. VTK binaries and source code are available at www.vtk.org.
Restart ImageJ

Related ImageJ Plugins

Collection of stack plugins.
VolumeJ - volume rendering in Java.
TransformJ - geometric transformations up to 4D.
DICOM input/output.