Cell shape analysis using the spherical harmonics decomposition
Project description
FlowShape
This package provides functionality for the analysis of cell shape using the spherical harmonics decomposition. Please refer to our paper "Cell shape characterization, alignment, and comparison using FlowShape" 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 demos, 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.
Further, demo_alignment.ipynb
shows how to align meshes.
demo_from_img.ipynb
shows how to use marching cubes to make meshes from image stacks.
There are some additional dependencies for this notebook.
How to use
See the demos for examples on how to use the package. The API consists only of functions operating on NumPy ndarrays and there are no classes. Most functions have docstrings in the source.
Citation
Bibtex:
@article{10.1093/bioinformatics/btad383,
author = {van Bavel, Casper and Thiels, Wim and Jelier, Rob},
title = "{Cell shape characterization, alignment, and comparison using FlowShape}",
journal = {Bioinformatics},
volume = {39},
number = {6},
pages = {btad383},
year = {2023},
month = {06},
issn = {1367-4811},
doi = {10.1093/bioinformatics/btad383},
url = {https://doi.org/10.1093/bioinformatics/btad383},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/39/6/btad383/50738096/btad383.pdf},
}
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