pywarper

pywarper is a Python package for conformal mapping-based warping of neuronal arbor morphologies, based on the MATLAB implementations (Sümbül, et al. 2014).

Installation

To install the latest tagged version:

pip install pywarper

Or to install the development version, clone the repository and install it with pip install -e:

git clone https://github.com/berenslab/pywarper.git
pip install -e pywarper

By default, pywarper uses scipy.sparse.linalg.spsolve to solve sparse matrices, which can be slow. For better performance, you can manually install the additional dependencies of scikit-sparse first:

# mac
brew install suite-sparse

# debian
sudo apt-get install libsuitesparse-dev

then:

pip install pywarper[scikit-sparse]

Usage

See the example notebook for usage.