pycellfit 0.0.6

Python implementation of the CellFIT method of inferring cellular forces

Project Description

pycellfit: an open-source Python implementation of the CellFIT method of inferring cellular forces developed by Brodland et al.

Author: Nilai Vemula, Vanderbilt University (working under Dr. Shane Hutson, Vanderbilt University)

Project Goal: To develop an open-source version of CellFIT, a toolkit for inferring tensions along cell membranes and pressures inside cells based on cell geometries and their curvilinear boundaries. (See [1].)

Project Timeline: Initial project started in August 2019 with work based off of XJ Xu. This repository was re-made in May 2020 in order to restart repository structure.

Project Status: Early development/Planning

Getting Started

This project is available on PyPI. For now, simply clone this repository and … ??

Making a development virtual environment (in Windows command prompt): Assuming you are in the base directory of this repository

> python -m venv pycellfit_dev

> pycellfit_dev\Scripts\activate

> pip install -r requirements_dev.txt

Dependencies

• numpy

• twine

Features

This section will include a list of features available in the package and maybe a check-list of things to add

Examples

This section will walk through an example of the basic pycellfit pipeline.

Future Goals

The final implementation of pycellfit will be as a web-app based on the Django framework.

References

[1]

Brodland GW, Veldhuis JH, Kim S, Perrone M, Mashburn D, et al. (2014) CellFIT: A Cellular Force-Inference Toolkit Using Curvilinear Cell Boundaries. PLOS ONE 9(6): e99116. https://doi.org/10.1371/journal.pone.0099116