QuantAn

Quantitative Analyser

Sample data

Install

Windows

• Use installer (experimental)

or

• Install Anaconda for python 2.7

• Install QuantAn

  conda install -c mjirik -c SimpleITK quantan
  

Linux (Ubuntu 14.04)

• Install prerequisites

  sudo apt-get install cmake libinsighttoolkit3-dev libpng12-dev libgdcm2-dev git wget
  wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
  source Miniconda-latest-Linux-x86_64.sh
  conda install numpy scipy pip imtools io3d sed3
  

• Install skelet3d package

  git clone https://github.com/mjirik/skelet3d.git
  cd skelet3d
  mkdir build
  cd build 
  cmake ..
  make 
  sudo make install
  pip install .
  

• Install Quantan

  conda install -c mjirik -c SimpleITK quantan
  

Mac OS

• Install prerequisites (brew packages, anaconda)

  ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
  brew install git cmake homebrew/science/insighttoolkit libpng
  curl "http://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh" -o "Miniconda-latest.sh"
  bash Miniconda-latest.sh -b
  echo "export PATH=$HOMEDIR/miniconda/bin:\$PATH" >> ~/.profile
  

• Install skelet3d package

  git clone https://github.com/mjirik/skelet3d.git
  cd skelet3d
  mkdir build
  cd build 
  cmake ..
  make 
  sudo make install
  cd ..
  pip install .
  

• Install Quantan

  conda install -c mjirik -c SimpleITK quantan
  

  Run

Run QuantAn with:

    python -m quantan

Sample data

Download sample data into sample_data directory

    quantan --get-sample-data

Sample outputs

• segmentation (DICOM)
• skeleton (DICOM)
• labeled skeleton (DICOM)