Medical image analysis framework merging ANTsPy and deep learning

Overview

Build Status Contributor Covenant

ANTsPyNet

A collection of deep learning architectures and applications ported to the python language and tools for basic medical image processing. Based on keras and tensorflow with cross-compatibility with our R analog ANTsRNet.

Documentation page https://antsx.github.io/ANTsPyNet/.

ANTsXNetTools

For MacOS and Linux, may install with:

pip install antspynet

Architectures

Image voxelwise segmentation/regression

Image classification/regression

Object detection

Image super-resolution

Registration and transforms

Generative adverserial networks

Clustering

Applications

Miscellaneous


Installation

  • ANTsPyNet Installation:
    • Option 1:
      $ git clone https://github.com/ANTsX/ANTsPyNet
      $ cd ANTsPyNet
      $ python setup.py install
      

Publications

  • Nicholas J. Tustison, Talissa A. Altes, Kun Qing, Mu He, G. Wilson Miller, Brian B. Avants, Yun M. Shim, James C. Gee, John P. Mugler III, and Jaime F. Mata. Image- versus histogram-based considerations in semantic segmentation of pulmonary hyperpolarized gas images. Magnetic Resonance in Medicine. (pubmed)

  • Nicholas J. Tustison, Philip A. Cook, Andrew J. Holbrook, Hans J. Johnson, John Muschelli, Gabriel A. Devenyi, Jeffrey T. Duda, Sandhitsu R. Das, Nicholas C. Cullen, Daniel L. Gillen, Michael A. Yassa, James R. Stone, James C. Gee, and Brian B. Avants for the Alzheimer’s Disease Neuroimaging Initiative. The ANTsX ecosystem for quantitative biological and medical imaging. Scientific Reports. 11(1):9068, Apr 2021. (pubmed)

  • Andrew T. Grainger, Arun Krishnaraj, Michael H. Quinones, Nicholas J. Tustison, Samantha Epstein, Daniela Fuller, Aakash Jha, Kevin L. Allman, Weibin Shi. Deep Learning-based Quantification of Abdominal Subcutaneous and Visceral Fat Volume on CT Images, Academic Radiology. (pubmed)

  • Nicholas J. Tustison, Brian B. Avants, and James C. Gee. Learning image-based spatial transformations via convolutional neural networks: a review, Magnetic Resonance Imaging, 64:142-153, Dec 2019. (pubmed)

  • Nicholas J. Tustison, Brian B. Avants, Zixuan Lin, Xue Feng, Nicholas Cullen, Jaime F. Mata, Lucia Flors, James C. Gee, Talissa A. Altes, John P. Mugler III, and Kun Qing. Convolutional Neural Networks with Template-Based Data Augmentation for Functional Lung Image Quantification, Academic Radiology, 26(3):412-423, Mar 2019. (pubmed)

  • Andrew T. Grainger, Nicholas J. Tustison, Kun Qing, Rene Roy, Stuart S. Berr, and Weibin Shi. Deep learning-based quantification of abdominal fat on magnetic resonance images. PLoS One, 13(9):e0204071, Sep 2018. (pubmed)

  • Cullen N.C., Avants B.B. (2018) Convolutional Neural Networks for Rapid and Simultaneous Brain Extraction and Tissue Segmentation. In: Spalletta G., Piras F., Gili T. (eds) Brain Morphometry. Neuromethods, vol 136. Humana Press, New York, NY doi

Acknowledgments

Owner
Advanced Normalization Tools Ecosystem
Ecosystem supporting multivariate / multiple modality medical image analytics across programming languages.
Advanced Normalization Tools Ecosystem
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