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Neural networks toolbox focused on medical image analysis
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README.md

neuron

A Neural networks toolbox with a focus on medical image analysis in tensorflow/keras for now.
Note: this is under ongoing development

Main tools

  • layers: various network layers, including a rich SpatialTransformer layer for N-D (dense and affine) spatial transforms, a vector integration layer VecInt, sparse operations (e.g. SpatiallySparse_Dense), and LocallyConnected3D currently not included in keras
  • utils: various utilities, including interpn: N-D gridded interpolation, transform: warp images, integrate_vec: vector field integration, stack_models: keras model stacking
  • models: flexible models (many parameters to play with) particularly useful in medical image analysis, such as UNet/hourglass model, convolutional encoders and decoders
  • generators: generators for medical image volumes and various combinations of volumes, segmentation, categorical and other output
  • callbacks: a set of callbacks for keras training to help with understanding your fit, such as Dice measurements and volume-segmentation overlaps
  • dataproc: a set of tools for processing medical imaging data for preparation for training/testing
  • metrics: metrics (most of which can be used as loss functions), such as Dice or weighted categorical crossentropy
  • vae_tools: tools for analyzing (V)AE style models
  • plot: plotting tools, mostly for debugging models

Requirements:

  • tensorflow, keras and all of their requirements (e.g. hyp5)
  • numpy, scipy, tqdm
  • pytools lib

Papers:

If you use this code, please cite:

Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation
Adrian V. Dalca, John Guttag, Mert R. Sabuncu
CVPR 2018.
[ PDF | arxiv | bibtex ]

If you are using any of the sparse/imputation functions, please cite:

Unsupervised Data Imputation via Variational Inference of Deep Subspaces
Adrian V. Dalca, John Guttag, Mert R. Sabuncu
Arxiv preprint 2019
[ arxiv | bibtex ]

Development:

Please open an issue [preferred] or contact Adrian Dalca at adalca@csail.mit.edu for question related to neuron.

Use/demos:

Parts of neuron were used in VoxelMorph and brainstorm, which we encourage you to check out!

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