Supplementary code for the paper Automatic motion estimation with applications to hiPSC-CMs

DOI

Supplementary code for the paper Automatic motion estimation with applications to hiPSC-CMs#

This repository contains supplementary code for reproducing results in the paper

Output of rendered notebooks are found at https://computationalphysiology.github.io/automatic-motion-estimation/README.html.

The code is heavily based on the library mps-motion. Please check out the documentation in that library for more details.

Running with binder#

If you want to run the examples without installing anything you can launch an interactive environment with Binder, by clicking the following button Binder

Running locally#

Python virtual environment#

To run the notebooks locally, you first need to install the necessary requirements. There are two options. Either, you can create a virtual environment with python

python3 -m venv venv

and activate it. On Unix (MacOSX and Linux) you do

. \venv/bin/activate

and on Windows you do

.\venv\Scripts\activate

Next you install the dependencies

python3 -m pip install -r requirements.txt

Docker#

We also provide two different docker images for you. In order to start a container you can use the docker run command. For example the command

docker run --rm -v $(pwd):/home/shared -w /home/shared -ti ghcr.io/computationalphysiology/automatic-motion-estimation:latest

will run the latest version and share your current working directory with the container. The source code of the repository is located at /repo in the docker container.

To run the notebooks, one can use ghcr.io/computationalphysiology/automatic-motion-estimation-lab:latest, i.e

docker run -ti -p 8888:8888 --rm ghcr.io/computationalphysiology/automatic-motion-estimation-lab:latest

to run interactively with Jupyter lab in browser.

Citing#

If you use this code in your research, please cite the following paper

@article{10.1088/2057-1976/ad7268,
	author={Finsberg, Henrik Nicolay Topnes and Charwat, Verena and Healy, Kevin E and Wall, Samuel},
	title={Automatic motion estimation with applications to hiPSC-CMs},
	journal={Biomedical Physics & Engineering Express},
	url={http://iopscience.iop.org/article/10.1088/2057-1976/ad7268},
	year={2024},
}
Contents