scikit-surgeryfred

FRED provides an interactive demonstration of fiducial based registration for teaching purposes

https://github.com/scikit-surgery/scikit-surgeryfred

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FRED provides an interactive demonstration of fiducial based registration for teaching purposes

README.rst

Fiducial Registration Educational Demonstration
===============================================

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   :alt: Logo

.. image:: https://github.com/SciKit-Surgery/scikit-surgeryfred/raw/master/tryfred.gif 
   :height: 128px
   :target: https://scikit-surgeryfred.ew.r.appspot.com/
   :alt: try fred

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   :target: https://github.com/SciKit-Surgery/scikit-surgeryfred/actions
   :alt: GitHub Actions CI status

.. image:: https://coveralls.io/repos/github/SciKit-Surgery/scikit-surgeryfred/badge.svg?branch=master&service=github
    :target: https://coveralls.io/github/SciKit-Surgery/scikit-surgeryfred?branch=master
    :alt: Test coverage

.. image:: https://readthedocs.org/projects/scikit-surgeryfred/badge/?version=latest
    :target: http://scikit-surgeryfred.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

.. image:: https://img.shields.io/badge/Read-SciKit--SurgeryFRED-informational
   :target: https://discovery.ucl.ac.uk/id/eprint/10112339/7/Thompson_115980U.pdf
   :alt: The SciKit-SurgeryFRED paper

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4314970.svg
   :target: https://doi.org/10.5281/zenodo.4314970
   :alt: DOI - Zenodo

.. image:: https://img.shields.io/badge/Video-SPIE2021-blueviolet
   :target: https://www.youtube.com/watch?v=PaXytDjojOI
   :alt: Our SPIE 2021 Talk

.. image:: https://img.shields.io/badge/Video-Registration-blueviolet
   :target: https://www.youtube.com/watch?v=t_6CH5uroYo
   :alt: Video Demonstration on YouTube

.. image:: https://img.shields.io/badge/Video-Game-blueviolet
   :target: https://www.youtube.com/watch?v=ansH1w2ST-g
   :alt: Video Demonstration of Game on YouTube

.. image:: https://img.shields.io/twitter/follow/scikit_surgery?style=social
   :target: https://twitter.com/scikit_surgery?ref_src=twsrc%5Etfw
   :alt: Follow scikit_surgery on twitter


Author: Stephen Thompson

This is the Fiducial Registration Educational Demonstration (SciKit-SurgeryFRED), part of the `SciKit-Surgery`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.

Fiducial Registration Educational Demonstration is intended to be used as part of an online tutorial in using fiducial based registration. The tutorial covers the basic theory of fiducial based registration, which is used widely in image guided interventions. The tutorial aims to help the students develop an intuitive understanding of key concepts in fiducial based registration, including Fiducial Localisation Error, Fiducial Registration Error, and Target Registration Error. 

Citing
------
If you use SciKit-SurgeryFRED in your research or teaching please cite our paper:

Stephen Thompson, Tom Dowrick, Mian Ahmad, Jeremy Opie, and Matthew J. Clarkson "Are fiducial registration error and target registration error correlated? SciKit-SurgeryFRED for teaching and research", Proc. SPIE 11598, Medical Imaging 2021: Image-Guided Procedures, Robotic Interventions, and Modeling, 115980U (15 February 2021); https://doi.org/10.1117/12.2580159 

Specific releases can be cited via the Zenodo tag. 

SciKit-Surgery can also be cited as:

Thompson S, Dowrick T, Ahmad M, et al. "SciKit-Surgery: compact libraries for surgical navigation." International Journal of Computer Assisted Radiology and Surgery. 2020 May. https://doi.org/10.1007/s11548-020-02180-5

Developing
----------

Cloning
^^^^^^^

You can clone the repository using the following command:

::

    git clone https://github.com/SciKit-Surgery/scikit-surgeryfred


Contributing
^^^^^^^^^^^^

Please see the `contributing guidelines`_.


Useful links
^^^^^^^^^^^^

* `Source code repository`_
* `Google Cloud Firestore (login required)`_
* `Google Cloud Console (login required)`_


Licensing and copyright
-----------------------

Copyright 2020 University College London.
Fiducial Registration Educational Demonstration is released under the BSD-3 license. Please see the `license file`_ for details.


Acknowledgements
----------------

Supported by `Wellcome`_ and `EPSRC`_.


.. _`Wellcome EPSRC Centre for Interventional and Surgical Sciences`: http://www.ucl.ac.uk/weiss
.. _`source code repository`: https://github.com/SciKit-Surgery/scikit-surgeryfred
.. _`Documentation`: https://scikit-surgeryfred.readthedocs.io
.. _`SciKit-Surgery`: https://github.com/SciKit-Surgery
.. _`University College London (UCL)`: http://www.ucl.ac.uk/
.. _`Wellcome`: https://wellcome.ac.uk/
.. _`EPSRC`: https://www.epsrc.ac.uk/
.. _`contributing guidelines`: https://github.com/SciKit-Surgery/scikit-surgeryfred/blob/master/CONTRIBUTING.rst
.. _`license file`: https://github.com/SciKit-Surgery/scikit-surgeryfred/blob/master/LICENSE
.. _`Google Cloud Firestore (login required)`: https://console.cloud.google.com/firestore/databases?hl=en&project=scikit-surgeryfred
.. _`Google Cloud Console (login required)` : https://console.cloud.google.com/home/dashboard?hl=en&project=scikit-surgeryfred

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use SciKit-SurgeryFRED packages in your research, please cite it as below."
authors:
- family-names: "Thompson"
  given-names: "Stephen"
  orcid: "https://orcid.org/0000-0001-7286-1326"
title: "SciKit-Surgery"
url: "https://github.com/SciKit-Surgery/scikit-surgery"
preferred-citation:
  type: article
  authors:
  - family-names: "Thompson"
    given-names: "Stephen"
    orcid: "https://orcid.org/0000-0001-7286-1326"
  - family-names: "Dowrick"
    given-names: "Thomas"
    orcid: "https://orcid.org/0000-0002-2712-4447"
  - family-names: "Ahmad"
    given-names: "Mian"
    orcid: "https://orcid.org/0000-0002-4706-4146"
  - family-names: "Opie"
    given-names: "Jeremy"
  - family-names: "Clarkson"
    given-names: "Matthew"
    orcid: "https://orcid.org/0000-0002-5565-1252"
  doi: 10.1117/12.2580159 
  journal: "Proc. SPIE Medical Imaging 2021: Image-Guided Procedures, Robotic Interventions, and Modeling"
  title: "Are fiducial registration error and target registration error correlated? SciKit-SurgeryFRED for teaching and research."
  volume: 11598
  issue: 11598oU
  year: 2021

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