MIC-DKFZ

Repositories

• batchgenerators

  A framework for data augmentation for 2D and 3D image classification and segmentation
  Jupyter Notebook Apache-2.0 112 522 10 2 Updated Sep 16, 2020

• nnUNet
  Python Apache-2.0 282 911 14 1 Updated Sep 16, 2020

• basic_unet_example

  An example project of how to use a U-Net for segmentation on medical images with PyTorch.
  Python Apache-2.0 26 78 1 0 Updated Sep 11, 2020

• Hyppopy

  Hyppopy is a python toolbox for blackbox optimization. It's purpose is to offer a unified and easy to use interface to a collection of solver libraries.
  Python 4 17 2 0 Updated Sep 8, 2020

• TractSeg

  Automatic White Matter Bundle Segmentation
  Python Apache-2.0 35 87 6 0 Updated Aug 28, 2020

• trixi

  Manage your machine learning experiments with trixi - modular, reproducible, high fashion. An experiment infrastructure optimized for PyTorch, but flexible enough to work for your framework and your tastes.

  visualization experiment machine-learning deep-neural-networks deep-learning example logging
  Python MIT 15 198 0 0 Updated Aug 26, 2020

• niicat

  This is a tool to quickly preview nifti images on the terminal
  Python GPL-2.0 3 26 3 0 Updated Aug 21, 2020

• MITK-Diffusion

  MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit

  simulation dicom registration segmentation modelling brain peak
  C++ 7 14 0 0 Updated Aug 19, 2020

• mood

  Repository for the Medical Out-of-Distribution Analysis Challenge at MICCAI 2020.
  Python Apache-2.0 2 26 1 0 Updated Jul 28, 2020

• n2c2-challenge-2019
  Jupyter Notebook Apache-2.0 0 1 0 0 Updated Jul 23, 2020

• medicaldetectiontoolkit

  The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

  deep-neural-networks deep-learning detection medical-imaging segmentation object-detection medical-image-computing
  Python Apache-2.0 216 820 23 3 Updated Jul 22, 2020

• RegRCNN

  This repository holds the code framework used in the paper Reg R-CNN: Lesion Detection and Grading under Noisy Labels. It is a fork of MIC-DKFZ/medicaldetectiontoolkit with regression capabilites.

  deep-learning detection object-detection medical-image-computing medical-image-processing mask-rcnn medical-image-analysis
  Python Apache-2.0 10 22 2 0 Updated Apr 27, 2020

• HD-BET

  MRI brain extraction tool
  Python Apache-2.0 8 38 3 0 Updated Mar 24, 2020

• cmdint

  CmdInterface enables detailed logging of command line and python experiments in a very lightweight manner (coding wise). It wraps your command line or python function calls in a few lines of python code and logs everything you might need to reproduce the experiment later on or to simply check what you did a couple of years ago.

  python lightweight logging reproducibility experiment-tracking
  Python Apache-2.0 0 8 0 0 Updated Feb 21, 2020

• MatchPoint

  MatchPoint is a translational image registration framework written in C++. It offers a standardized interface to utilize several registration algorithm resources (like ITK, plastimatch, elastix) easily in a host application.
  C++ 1 0 0 0 Updated Feb 17, 2020

• LIDC-IDRI-processing

  Scripts for the preprocessing of LIDC-IDRI data
  Python MIT 13 44 8 0 Updated Dec 17, 2019

• vae-anomaly-experiments
  Python Apache-2.0 2 17 0 0 Updated Dec 6, 2019

• PROUNET

  Prostate U-net
  Python GPL-3.0 0 4 2 0 Updated Sep 10, 2019

• RTTB

  Swiss army knife for radiotherapy analysis

  dicom-rt dose radiotherapy medical-physics anaylsis dose-statistics
  C++ BSD-3-Clause 5 11 0 0 Updated May 27, 2019

• probabilistic_unet

  A U-Net combined with a variational auto-encoder that is able to learn conditional distributions over semantic segmentations.
  Jupyter Notebook Apache-2.0 5 15 0 0 Updated Dec 17, 2018

• BraTS2017
  Python Apache-2.0 17 59 2 1 Updated Oct 10, 2018

• ACDC2017
  Python Apache-2.0 11 23 1 0 Updated Oct 10, 2018