*****
WORC
*****

Workflow for Optimal Radiomics Classification
---------------------------------------------

WORC is an open-source python package for the easy execution of end-to-end
radiomics pipelines.

We aim to establish a general radiomics platform supporting easy
integration of other tools. With our modular build and support of
different software languages (Python, MATLAB, R, executables etc.), we want
to facilitate and stimulate collaboration, standardisation and
comparison of different radiomics approaches. By combining this in a
single framework, we hope to find an universal radiomics strategy that
can address various problems.

WORC is open-source (licensed under the Apache 2.0 license) and hosted on Github at `https://github.com/MStarmans91/WORC <https://github.com/MStarmans91/WORC>`_

For support, go to the issues on the Gibhub page: `https://github.com/MStarmans91/WORC/issues <https://github.com/MStarmans91/WORC/issues>`_

To get yourself a copy, see the :ref:`installation-chapter`

The official documentation can be found at `WORC.readthedocs.io <http://WORC.readthedocs.io>`_

For Tutorials on WORC, both for beginner and advanced WORCflows, please

see our Tutorial repository https://github.com/MStarmans91/WORCTutorial.


The article on WORC is currently in press. WORC has been presented in the following:

    `M. P. A. Starmans, S. R. van der Voort, M. Vos, F. Incekara, J. J. Visser, M. Smits, M. G. Thomeer, W. J. Niessen and S. Klein. "Fully automatic construction of optimal radiomics workflows." European Conference of Radiology (ECR) 2019. <https://ecronline.myesr.org/ecr2019/index.php?p=recording&t=recorded&lecture=fully-automatic-construction-of-optimal-radiomics-workflows>`_

    `Martijn P. A. Starmans, Sebastian R. van der Voort, Razvan L. Miclea, Melissa Vos, Fatih Incekara, Milea J.M. Timbergen, Maarten M.J. Wijnenga, Guillaume A. Padmos, G.H.J. van Leenders, George Kapsas, Martin J. van den Bent, Arnaud J.P.E. Vincent, Dirk J. Grünhagen, Cornelis Verhoef, Stefan Sleijfer, Jacob J. Visser, Marion Smits, Maarten, G. Thomeer, Wiro J. Niessen, and Stefan Klein. "Harmonizing radiomics among applications through adaptive workflow optimization." European Society of Medical Imaging Informatics (EuSoMII) Annual Meeting 2019. <https://www.eusomii.org/events/eusomii-annual-meeting-2018/>`_

WORC has been used in the following studies:

    `M. P. A. Starmans, R. Miclea, S. R. van der Voort, W. J. Niessen, M. G. Thomeer and S. Klein. "Classification of malignant and benign liver tumors using a radiomics approach." Proceedings Volume 10574, Medical Imaging 2018: Image Processing; 105741D (2018) . <https://doi.org/10.1117/12.2293609>`_

    `Milea J.M. Timbergen*, Martijn P. A. Starmans*, Melissa Vos, Sebastian R. van der Voort, Guillaume A. Padmos, Wouter Kessels, Wiro J. Niessen, Geert J.L.H. van Leenders, Dirk J. Grünhagen, Stefan Sleijfer, Cornelis Verhoef, Stefan Klein and Jacob J. Visser. "Mutation stratification of desmoid-type fibromatosis using a Radiomics approach." Desmoid Tumor Research Foundation (DTRF) 2018. <https://dtrf.org/wp-content/uploads/2018/10/Timbergen-2018.pdf>`_

    `Melissa Vos*, Martijn P. A. Starmans*, Milea J.M. Timbergen, Sebastian R. van der Voort, Guillaume A. Padmos, Wouter Kessels, Wiro J. Niessen, Geert J.L.H. van Leenders, Dirk J. Grünhagen, Stefan Sleijfer, Cornelis Verhoef, Stefan Klein and Jacob J. Visser. "Differentiating well-differentiated liposarcomas from lipomas using a Radiomics approach." ConnectiveTissueOncologySociety (CTOS) 2018.`_

    `Milea J.M. Timbergen*, Martijn P. A. Starmans*, Melissa Vos, Sebastian R. van der Voort, Guillaume A. Padmos, Wouter Kessels, Wiro J. Niessen, Geert J.L.H. van Leenders, Dirk J. Grünhagen, Stefan Sleijfer, Cornelis Verhoef, Stefan Klein and Jacob J. Visser. "Mutation stratification of desmoid-type fibromatosis using a Radiomics approach." ConnectiveTissueOncologySociety (CTOS) 2018.`_

    `Martijn P. A. Starmans, Sebastian R. van der Voort, Razvan L. Miclea, Melissa Vos, Fatih Incekara, Milea J.M. Timbergen, Maarten M.J. Wijnenga, Guillaume A. Padmos, Wouter Kessels, G.H.J. van Leenders, George Kapsas, Martin J. van den Bent, Arnaud J.P.E. Vincent, Dirk J. Grünhagen, Cornelis Verhoef, Stefan Sleijfer, Jacob J. Visser, Marion Smits, Maarten, G. Thomeer, Wiro J. Niessen, and Stefan Klein. "Fully Automatic Construction of Optimal Radiomics Workflows ." Bio-Medical Engineering (BME) Conference 2019. <https://www.bme2019.nl/mobview/presentation/58/>`_

    `M. P. A. Starmans, R. Miclea, S. R. van der Voort, W. J. Niessen, S. Klein and M. G. Thomeer. "Classification of malignant and benign liver tumours using a radiomics approach." European Conference of Radiology (ECR) 2019. <https://ecronline.myesr.org/ecr2019/index.php?p=recording&t=recorded&lecture=classification-of-malignant-and-benign-liver-tumours-using-a-radiomics-approach>`_

    `M. P. A. Starmans, A. Blazevic, S. R. van der Voort, T. Brabander, J. Hofland, W. J. Niessen, W. W. de Herder and S. Klein. "Prediction of surgery requirement in mesenteric fibrosis on CT using a radiomics approach." European Conference of Radiology (ECR) 2019. <https://ecronline.myesr.org/ecr2019/index.php?p=recording&t=recorded&lecture=prediction-of-surgery-requirement-in-mesenteric-fibrosis-on-ct-using-a-radiomics-approach>`_

    `Jose M. Castillo T., Martijn P. A. Starmans, Ivo Schoots, Wiro J. Niessen, Stefan Klein, Jifke F. Veenland. "CLASSIFICATION OF PROSTATE CANCER: HIGH GRADE VERSUS LOW GRADE USING A RADIOMICS APPROACH." IEEE International Symposium on Biomedical Imaging (ISBI) 2019. <https://embs.papercept.net/conferences/conferences/ISBI19/program/ISBI19_ContentListWeb_3.html>`_

WORC is made possible by contributions from the following people: Martijn Starmans, Thomas Phil, and Stefan Klein


WORC Documentation
===================
.. toctree::
    :maxdepth: 3
    :glob:

    static/introduction.rst
    static/quick_start.rst
    static/user_manual.rst
    static/configuration.rst
    static/file_description.rst
    static/changelog.rst

WORC User reference
====================

.. toctree::
    :maxdepth: 3
    :glob:

    user_reference/*

WORC Developer Module reference
================================
.. toctree::
   :maxdepth: 4

   autogen/WORC



Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
