Home

ImageAnalysisTools is a java library developed for processing and quantifying biological microscopy images. We use it particularly for the identification and quantification of centromeres and kinetochores, but the underlying infrastructure, can be used for building tools to process any type of image.

Besides providing prebuilt tools for quantifying centromeres, the library has two major goals:

1. Providing a high-level interface that facilitates rapid development of application-specific image analysis tools: In particular, common image processing needs like visiting all pixels in an image or applying common filters can be accomplished with very little code and only a very simple interface to learn. Complete javadoc for the interface is provided at every release.
2. Record keeping: analysis methods run with the library produce an output metadata file that keeps a record of what was done, which images were used for input, what output was generated, and (soon) exactly what version of the software was run. This record is both human- and machine-readable, and is stored in the same format as files used to specify input parameters, so the same analysis can be run again simply by using output files as input files.

The library consists of two package hierarchies: ...imageanalysistools, which contains all the library functionality, and ...analysistoolsinterface, which contains a GUI and runs as an ImageJ/FIJI plugin.

For more information on using the project from the GUI see Using ImageAnalysisTools.

It is possible to build new analysis methods at runtime without any additional programming by using the GUI. For documentation, see creating analysis methods at runtime. It is also possible to script new analysis methods using jruby; see scripting with jruby

For more information on using the project as a library from your own code see Developing with ImageAnalysisTools.

Full javadoc for the library is available with every stable release.