automatic-motion-estimation

Source code for reproducing results in the paper "Automatic motion estimation with applications to hiPSC-CMs"

https://github.com/computationalphysiology/automatic-motion-estimation

Science Score: 67.0%

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CITATION.cff file
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DOI references
Found 3 DOI reference(s) in README
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Links to: iop.org, zenodo.org
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Low similarity (14.5%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Source code for reproducing results in the paper "Automatic motion estimation with applications to hiPSC-CMs"

Basic Info

Host: GitHub
Owner: ComputationalPhysiology
License: mit
Language: Jupyter Notebook
Default Branch: main
Homepage: https://computationalphysiology.github.io/automatic-motion-estimation/
Size: 58.6 KB

Statistics

Stars: 0
Watchers: 3
Forks: 0
Open Issues: 0
Releases: 1

Created over 2 years ago · Last pushed over 1 year ago

Metadata Files

Readme License Citation

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}, }

Owner

Name: Computational Physiology at Simula Research Laboratory
Login: ComputationalPhysiology
Kind: organization
Location: Fornebu, Norway

Website: https://computationalphysiology.github.io
Repositories: 51
Profile: https://github.com/ComputationalPhysiology

GitHub organization for the computational physiology department at Simula Research Laboratory

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Fisberg"
  given-names: "Henrik"
  orcid: "https://orcid.org/0000-0003-3766-2393"
title: "automatic-motion-estimation"
version: 1.0.0
doi: 10.5281/zenodo.1234
date-released: 2024-08-27
url: "https://github.com/ComputationalPhysiology/automatic-motion-estimation"
preferred-citation:
  type: article
  doi: "10.1088/2057-1976/ad7268"
  journal: "Biomedical Physics & Engineering Express"
  title: "Automatic motion estimation with applications to hiPSC-CMs"
  year: 2024
  authors:
  - family-names: "Fisberg"
    given-names: "Henrik"
    orcid: "https://orcid.org/0000-0003-3766-2393"
  - family-names: "Charwat"
    given-names: "Verena"
  - family-names: "Healy"
    given-names: "Kevin E."
  - family-names: "Wall"
    given-names: "Samuel T."

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