Installation

Again, two options are offered. One can first download a compiled version of the Fiji plugin and try out B-recs in a minute. In that case, you simply need to put the provided .jar file in the Plugin folder of your Fiji / Image J package. The second option is to compile yourself B-recs. This is a more difficult task although scripts are provided to ease the process. The major advantage of the second option is that you can then run B-recs from the command line and the code is optimized for your system: it allows optimal performances (see also code implementation)..

Requirements

A few standard libraries are required:

  • cmake: Building tool for the package
  • libbz2: each reconstructed image is stored as a raw image compressed with Bzip2 (when asked on the command line).
  • libtiff: Brecs accepts input in tiff or raw format. All the results are output in the tiff format.
  • fftw3: Fourier transforms are not used in the algorithms itself but only in the preprocessing of the datasets, in order to define regions of interests whereby the algorithm is applied.
  • JNI: This is used in order to compile the java plugin.
  • Sphinx: this is the format of the present documentation. You need this library to generate the documentation

Quick install

mkdir build
cd build
cmake .. -DCMAKE_C_FLAGS_RELEASE="-O3 -march=native -mtune=native"
make
make install

You should then be able to run brecs-reconssparse --version. You can also adapt the place where the program is install by adjusting the prefix:

cmake -DCMAKE_INSTALL_PREFIX:PATH=/install/folder ..

Mac OS X

A homebrew formula is provided in order to ease the process. Start by installing Homebrew. Place the file packages/brecs.rb from the B-recs repository in the Formula folder, usually /usr/local/Library/Formula Then, simply execute brew install brecs. You should then be able to run the command line version of B-recs brecs-reconssparse.

Development version

If you use the development version available on bitbucket, the install process is very similar. Refer to the cmake documentation for more details.