It is highly recommended to install the project into a new virtual environment.

Python Requirements

The project is only available for Python 3.7. The main reason for this restriction is an external dependency ANTsPy that does not provide many precompiled wheels on PyPI.

External Dependencies

Some of the functionalities of atlalign depend on the TensorFlow implementation of the Learned Perceptual Image Patch Similarity. Unfortunately, the package is not available on PyPI and must be installed manually as follows.

pip install git+

You can now move on to installing the actual atlalign package!

Installation from PyPI

The atlalign package can be easily installed from PyPI.

pip install atlalign

Installation from source

As an alternative to installing from PyPI, if you want to try the latest version you can also install from source.

pip install git+

Development installation

For development installation one needs additional dependencies grouped in extras_requires in the following way:

  • dev - pytest + plugins, flake8, pydocstyle, tox

  • docs - sphinx

git clone
cd atlas_alignment
pip install -e .[dev,docs]

Generating documentation

To generate the documentation make sure you have dependencies from extras_requires - docs.

cd docs
make clean && make html

One can view the docs by opening docs/_build/html/index.html in a browser.