FARSIGHT Tutorials/Building Software/Bio-Formats/Building ITK Plugin

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The Bio-Formats ITK plugin provides an ImageIO plugin for ITK that uses Bio-Formats to read and write supported life sciences file formats.

The implementation is still very preliminary, and may be substantially changed before a stable release is announced. The plugin has been tested and works on Mac OS X and Linux. We have also compiled it successfully with Visual C++ on Windows, but there may be runtime issues.


Prerequisites

You must first build the following packages:


Compiling the plugin

  1. Change to the components/native/bf-itk directory of your LOCI Software source code checkout.
  2. Run the Ant build script: 
ant -Djace.home=/path/to/jace -Ditk.home=/path/to/itk/build


Build results

After the build succeeds, you can copy dependent libraries (BioFormatsIO.so, libjace.so, libbfcpp.so, jace-runtime.jar and loci_tools.jar) into the proper locations by executing: 

ant -Djace.home=/path/to/jace -Ditk.home=/path/to/itk/build dist

The script will suggest some commands to proceed in testing. These commands boil down to: a) set ITK_AUTOLOAD_PATH; b) run ImageHistogram1 example program on a TIFF file; c) optionally, clear ITK_AUTOLOAD_PATH and rerun to compare against the results with ITK's built-in TIFF reader.

Please direct questions to the Bio-Formats team.

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