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Algorithms for diffraction tomography

Project Description

PyPI Version Tests Status Coverage Status Docs Status

ODTbrain provides image reconstruction algorithms for Optical Diffraction Tomography with a Born and Rytov Approximation-based Inversion to compute the refractive index (n) in 2D and in 3D.


The documentation, including the reference and examples, is available on



Mac OS X


Install the FFTW3 and Python libraries. For Python 2.7, run

sudo port selfupdate
sudo port install fftw-3 py27-numpy py27-scipy py27-pyfftw pip
sudo easy_install pip
sudo pip install odtbrain


Install the FFTW3 and Python libraries. For Python 2.7, run

sudo brew tap homebrew/python
sudo brew update && brew upgrade
sudo brew install python --framework
sudo brew install fftw numpy scipy
sudo easy_install pip
sudo pip install odtbrain


  • Install the Anaconda version matching your architecture (32-bit or 64-bit).

  • Install PyFFTW using the corresponding installer at PyPI.

  • Finally:

    pip install odtbrain


Install the following packages:

  • for Python 2.7:

    sudo apt-get install libfftw3-3 libfftw3-dev python-cffi python-numpy python-pip python-scipy`
  • for Python 3.4:

    sudo apt-get install libfftw3-3 libfftw3-dev python3-cffi python3-numpy python3-pip python3-scipy``
  • Install the PyFFTW package. Depending on your distribution, the package name is either python-fftw3, python3-fftw3 (old) or python-pyfftw, python3-pyfftw (new). Attention: The package python-fftw provides a different FFTW library that is not used by ODTbrain. Alternatively, install from PyPI:

    pip install pyfftw
  • Finally:

    pip install odtbrain

Known Problems

  • For older versions of Ubuntu, the C foreign function interface``python-cffi`` is not available. Install the following packages
sudo apt-get install python-dev libffi-dev

and install cffi and numpy > 1.7.0 via pip, e.g.

pip install cffi
pip install numpy==1.7.0


Note: The tests may fail for some Python installations. Please check the algorithms by running the examples or update your distribution to the latest version.

After cloning into odtbrain, create a virtual environment

virtualenv --system-site-packages ve
source ve/bin/activate

Install all dependencies

python develop

Running an example

python examples/

Running tests

python test

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Filename, size & hash SHA256 hash help File type Python version Upload date
odtbrain-0.1.8-py2.py3-none-any.whl (41.0 kB) Copy SHA256 hash SHA256 Wheel py2.py3 Oct 3, 2017
odtbrain-0.1.8.tar.gz (891.2 kB) Copy SHA256 hash SHA256 Source None Oct 3, 2017

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