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

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},
}