flowshape 0.1.3

Cell shape analysis using the spherical harmonics decomposition

FlowShape

This package provides functionality for the analysis of cell shape using the spherical harmonics decomposition. Please refer to the preprint for more information. A local branch of lie_learn that does not depend on cython is included (spheremesh/lie_learn).

Installation

Currently the package is on pypi, but still requires conda to install libigl. We are working on an easier installation but in the meantime you can follow these steps:

Recommended: create a seperate conda environment and activate it:

conda create --name flowshape_env

conda activate flowshape_env

Then, install libigl from conda-forge:

conda install -c conda-forge igl

Finally, install FlowShape from pip:

pip install flowshape

Demo

For the demo, you will need JupyterLab, as well as Meshplot for plotting.

To install both, run:

conda install -c conda-forge jupyterlab meshplot

Then, to open JupyterLab, run:

jupyter-lab

Download the demo folder from this repository and open the demo.ipynb notebook.

How to use

See demo.ipynb for a basic example. The API consists only of functions operating on NumPy ndarrays and there are no classes. Most functions have docstrings in the source. More documentation to follow.