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The Insight Toolkit (ITK) is a cross-platform, open-source application development framework widely used for the development of image segmentation and image registration programs.
ITK integration with ImageJ
Although ITK is a C++ application, many ITK functions are available in ImageJ through the SimpleITK Java compatibility layer.
Enabling this functionality in ImageJ is simply a matter of turning on the ImageJ-ITK update site. Note that this will trigger a large download, as it requires the SimpleITK native library (up to a few hundred MB).
What’s on the update site?
SimpleITK 0.90 is distributed with this update. After update all SimpleITK classes can be called from the script editor.
When using @itkImage parameters in scripts, ImageJ Dataset objects will be automatically converted to SimpleITK Image objects.
There are several templates in the Script Editor demonstrating ITK use. The following example shows how to perform Otsu multilevel threshold using SimpleITK.
# @itkImage image
# @OUTPUT Dataset output
from org.itk.simple import OtsuMultipleThresholdsImageFilter
otsu = OtsuMultipleThresholdsImageFilter()
# call otsu using simple itk wrapper
output = otsu.execute(image, 2, 0, 255, True)
Developer resources
- GitHub (we welcome pull requests)
- An ImageJ2 Op that uses SimpleITK
- An ImageJ2 command (plugin that adds a menu item) for the Op.
Publication
To cite ITK, please use the following publication:
doi:10.3233/978-1-60750-929-5-586
See also:
