[en] Medical image analysis plays a key role in precision medicine. Data curation and pre-processing are critical steps in quantitative medical image analysis that can have a significant impact on the resulting performance of machine learning models. In this work, we introduce the Precision-medicine-toolbox, allowing clinical and junior researchers to perform data curation, image pre-processing, radiomics extraction, and feature exploration tasks with a customizable Python package. With this open-source tool, we aim to facilitate the crucial data preparation and exploration steps, bridge the gap between the currently existing packages, and improve the reproducibility of quantitative medical imaging research.
Disciplines :
Computer science
Author, co-author :
Lavrova, Elizaveta ; Université de Liège - ULiège > GIGA ; The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
Primakov, Sergey; The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
Salahuddin, Zohaib; The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
Beuque, Manon; The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
Verstappen, Damon; The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
Woodruff, Henry C.; The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands ; Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre, Maastricht, Netherlands
Lambin, Philippe; The D-Lab, Department of Precision Medicine, GROW—School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands ; Department of Radiology and Nuclear Medicine, Maastricht University Medical Centre, Maastricht, Netherlands
Language :
English
Title :
Precision-medicine-toolbox: An open-source python package for the quantitative medical image analysis[Formula presented]
The authors would like to thank the Precision Medicine department colleagues and external users for the feedback, Mart Smidt for testing the tool on the different data, 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.
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