ITK Release 4/Microscopy/File Formats/Bio-Formats

This page describes the process of building the ITK adaptors to the Bio-Format library.

Download JACE

Check out the Jace source code:

   svn co -r 39 https://jace.svn.sourceforge.net/svnroot/jace/trunk /path/to/jace

Where

   /path/to/jace 

is the desired location of your Jace source code checkout.

The "-r 39" matters, since Jace revisions 40 and later may not work with bf-cpp. As of this writing, the most recent revision was 52, and it does not compile on some systems. We currently recommend revision 39.

Download Bio-Formats

Download the bio-formats code according to the instructions in

  http://www.loci.wisc.edu/bio-formats/source-code

Essentially

  git clone git://dev.loci.wisc.edu/bio-formats.git

Build Bio-Formats and Its C++ Bindings

go to the top directory of the bio-formats source tree and type

   ant tools

then go to the directory "components/native/bf-cpp"

   cd components/native/bf-cpp 

and type

   ant   -Djace.home=/path/to/jace

where "/path/to/jace" is the path to the directory where you checked out the code of JACE.

This will produce C++ libraries that wrap the functionalities of the Bio-Formats Java library.

Configure ITK

Go to the binary tree where you have build ITK and rerun CMake

For example, in Linux do

     make   edit_cache

Go to the Advanced mode by hitting the "t" key.

Search for the CMake option

    ITKIO_SUPPORTS_BIOFORMATS_IMAGEIO

and turn it ON

reconfigure by hitting the "c" key.

At this point, new options will be displayed.

In particular:

 BIOFORMATS_CPP_LIB
 BIOFORMATS_JACE_LIB
 BIOFORMATS_INCLUDE_PATH

They should respectively point to

the libbfcpp.so library, the libjace.so and the "include" directory of the bf-cpp binding code.

For example, in a typical case, they will be:

 BIOFORMATS_CPP_LIB:FILEPATH=/home/ibanez/src/bio-formats/components/native/bf-cpp/build/libbfcpp.so
 BIOFORMATS_INCLUDE_PATH:PATH=/home/ibanez/src/bio-formats/components/native/bf-cpp/include
 BIOFORMATS_JACE_LIB:FILEPATH=/home/ibanez/src/bio-formats/components/native/bf-cpp/build/libjace.so