precision-medicine-toolbox 0.11

Precision medicine tool-box for medical imaging research

Welcome to precision-medicine-toolbox documentation!

precision-medicine-toolbox is an open-source python package for medical imaging data preparation for data science tasks. This package is aimed to provide a tool to curate the imaging data and to perform exploratory feature analysis.

If you are using this toolbox, please, cite the original paper:
Primakov, Sergey, Elizaveta Lavrova, Zohaib Salahuddin, Henry C. Woodruff, and Philippe Lambin. "Precision-medicine-toolbox: An open-source python package for facilitation of quantitative medical imaging and radiomics analysis." arXiv preprint arXiv:2202.13965 (2022).

Currently, the toolbox has the following functionality:

• Dataset exploration. This function gets the specified metadata from the DICOM files of the dataset and allows for exploration of the diversity degree of the imaging parameters..
• Dataset quality check. This function checks every scan in the dataset to be in line with the pre-defined requirements:
  • imaging modality is correct,
  • slice thickness is in the acceptable range,
  • number of slices is in the acceptable range,
  • all the slices have a target plane resolution,
  • in-plane pixel spacing is in the acceptable range,
  • reconstruction kernel for CT data is presented and is acceptable.
• Conversion of DICOM to NRRD. This function allows for the conversion of DICOM (CT or MR) dataset into volume (NRRD format) dataset. 2D data is temporarily not supported.
• Basic image pre-processing. This function performs basic image pre-processing steps, selected by the user; the following methods are available:
  • N4 bias field correction,
  • intensity rescaling, based on fat values or percentile values,
  • histogram matching,
  • intensities resampling,
  • histogram equalization,
  • Z-scoring, based on defined normalization coefficients or image-based values,
  • image reshaping.
• Unrolling NRRD images & ROI masks into jpeg slices. This function could be used for a quick check of the converted images or any existing NRRD/MHA dataset. It will generate the JPEG images for each ROI slice.
• Extracting of radiomics features. Feature extraction procedure using pyradiomics to obtain the radiomics features for NRRD/MHA dataset.
• Basic analysis of radiomics features. Export to Excel file of features basic statistics and statistical tests values and visualization (in .html report) of:
  • features values distributions in binary classes,
  • Shapiro-Wilk test for normality check,
  • features mutual correlation (Spearman) matrix,
  • p-values (corrected) for Mann-Whitney test for features mean values in groups,
  • univariate ROC-curves for each feature,
  • volumetric analysis: volume-based precision-recall curve + features correlation with volume.
• Binary classification metrics reporting. Given true labels and predicted probabilities, this function performs:
  • classification metrics reporting,
  • confusion matrices and ROC curves plotting.

Warning! Not intended for clinical use!

Code and documentation

precision-medicine-toolbox is an open-source package, the source code is available online. The online documentation is available here. The functionality of the toolbox is illustrated in the tutorial notebooks.

3rd-party packages used in precision-medicine-toolbox

Our package is using the existing quality tools for the key steps:

• pydicom (DICOM I/O),
• SimpleITK (image I/O and pre-processing),
• pyradiomics (features extraction).

See requirements.txt for more.

Installation

Before use, install the dependencies from the requirements file:

pip install -r requirements.txt   

Then clone repository with the git client of your preference.

The latest version is also available at PyPi:

pip install precision-medicine-toolbox   

Quick start

The following example illustrates how to initialize an object of a dataset class:

import os, sys
sys.path.append('path to precision-medicine-toolbox directory')
from pmtool.ToolBox import ToolBox

# set up parameters for your imaging dataset
parameters = {'data_path': 'root directory of the imaging data',
              'data_type': 'dcm', # DICOM data
              'multi_rts_per_pat': False # looks at 1 RTStruct/patient only
              }
my_dataset = ToolBox(**parameters)

Contributing

You can contribute to this package at our GitHub by:

• reporting the issues,
• giving us feedback for the code and the documentation via suggestions/comments:
  • directly in the Pull request,
  • writing and leaving a comment in the Conversation tab,
  • sending an e-mail to authors.

Authors and citation

Initial and main developers:

• Sergey Primakov @primakov
• Lisa Lavrova @lavrovaliz

Also you can see the list of the contributors.

License

This project is licensed under the BSD-3-Clause License (see the LICENSE for the details).

Acknowledgements

The authors would like to thank:

• the Precision Medicine department colleagues for their support and feedback,
• Mart Smidt for testing the tool on the different data,
• external users for the feedback,
• PyRadiomics for a reliable open-source tool for features extraction,
• Hugo Aerts et al. for the Lung1 dataset we used to demonstrate our functionality and The Cancer Imaging Archive for the publically available data.