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Welcome to pyradiomics documentation!

This is an open-source python package for the extraction of Radiomics features from medical imaging. With this package we aim to establish a reference standard for Radiomic Analysis, and provide a tested and maintained open-source platform for easy and reproducible Radiomic Feature extraction. By doing so, we hope to increase awareness of radiomic capabilities and expand the community. The platform supports both the feature extraction in 2D and 3D and can be used to calculate single values per feature for a region of interest ("segment-based") or to generate feature maps ("voxel-based").

If you publish any work which uses this package, please cite the following publication: van Griethuysen, J. J. M., Fedorov, A., Parmar, C., Hosny, A., Aucoin, N., Narayan, V., Beets-Tan, R. G. H., Fillon-Robin, J. C., Pieper, S., Aerts, H. J. W. L. (2017). Computational Radiomics System to Decode the Radiographic Phenotype. Cancer Research, 77(21), e104–e107. `https://doi.org/10.1158/0008-5472.CAN-17-0339 <https://doi.org/10.1158/0008-5472.CAN-17-0339>`_

Note

This work was supported in part by the US National Cancer Institute grant 5U24CA194354, QUANTITATIVE RADIOMICS SYSTEM DECODING THE TUMOR PHENOTYPE.

Warning

Not intended for clinical use.

Join the Community!

Join the PyRadiomics community on google groups here.

Table of Contents

Home <self>

installation usage customization radiomics features removedfeatures contributing developers labs FAQs <faq> changes

Feature Classes

Currently supports the following feature classes:

  • :pyFirst Order Statistics <radiomics.firstorder.RadiomicsFirstOrder>
  • :pyShape-based (3D) <radiomics.shape.RadiomicsShape>
  • :pyShape-based (2D) <radiomics.shape2D.RadiomicsShape2D>
  • :pyGray Level Co-occurrence Matrix <radiomics.glcm.RadiomicsGLCM> (GLCM)
  • :pyGray Level Run Length Matrix <radiomics.glrlm.RadiomicsGLRLM> (GLRLM)
  • :pyGray Level Size Zone Matrix <radiomics.glszm.RadiomicsGLSZM> (GLSZM)
  • :pyNeigbouring Gray Tone Difference Matrix <radiomics.ngtdm.RadiomicsNGTDM> (NGTDM)
  • :pyGray Level Dependence Matrix <radiomics.gldm.RadiomicsGLDM> (GLDM)

On average, Pyradiomics extracts  ≈ 1500 features per image, which consist of the 16 shape descriptors and features extracted from original and derived images (LoG with 5 sigma levels, 1 level of Wavelet decomposistions yielding 8 derived images and images derived using Square, Square Root, Logarithm and Exponential filters).

Detailed description on feature classes and individual features is provided in section radiomics-features-label.

Filter Classes

Aside from the feature classes, there are also some built-in optional filters:

  • :pyLaplacian of Gaussian <radiomics.imageoperations.getLoGImage> (LoG, based on SimpleITK functionality)
  • :pyWavelet <radiomics.imageoperations.getWaveletImage> (using the PyWavelets package)
  • :pySquare <radiomics.imageoperations.getSquareImage>
  • :pySquare Root <radiomics.imageoperations.getSquareRootImage>
  • :pyLogarithm <radiomics.imageoperations.getLogarithmImage>
  • :pyExponential <radiomics.imageoperations.getExponentialImage>
  • :pyGradient <radiomics.imageoperations.getGradientImage>
  • :pyLocal Binary Pattern (2D) <radiomics.imageoperations.getLBP2DImage>
  • :pyLocal Binary Pattern (3D) <radiomics.imageoperations.getLBP3DImage>

For more information, see also radiomics-imageoperations-label.

Supporting reproducible extraction

Aside from calculating features, the pyradiomics package includes additional information in the output. This information contains information on used image and mask, as well as applied settings and filters, thereby enabling fully reproducible feature extraction. For more information, see radiomics-generalinfo-label.

3rd-party packages used in pyradiomics

  • SimpleITK (Image loading and preprocessing)
  • numpy (Feature calculation)
  • PyWavelets (Wavelet filter)
  • pykwalify (Enabling yaml parameters file checking)
  • six (Python 3 Compatibility)

See also the requirements file.

Installation

PyRadiomics is OS independent and compatible with and Python >=3.5. Pre-built binaries are available on PyPi and Conda. To install PyRadiomics, ensure you have python installed and run:

  • python -m pip install pyradiomics

For more detailed installation instructions and building from source, see radiomics-installation-label section.

Pyradiomics Indices and Tables

  • modindex
  • genindex
  • search

License

This package is covered by the open source 3-clause BSD License.

Developers

1Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 2Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 3Department of Radiology, Netherlands Cancer Institute, Amsterdam, The Netherlands, 4GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands, 5Kitware, 6Isomics

Contact

We are happy to help you with any questions. Please contact us on the Radiomics community section of the 3D Slicer Discourse.

We'd welcome your contributions to PyRadiomics. Please read the contributing guidelines <radiomics-contributing-label> on how to contribute to PyRadiomics. Information on adding / customizing feature classes and filters can be found in the radiomics-developers section.