This is a collection of IPython Notebooks, designed for tutorials, presentations and to demonstrate using SimpleITK in the IPython Notebook with scipy environment for interactive image process.
SimpleITK is an abstraction layer and wrapper around the Insight Toolkit for many languages including python.
- 01 Image Basics
- 02 Pythonic Image
- 10 plotlib's imshow
- 20 Expand With Interpolators
- 21 Transform and Resampling
- 30 Segmentation Region Growing
- 31 Levelset Segmentation
- 32 Watershed Segmentation
- 41 Progress
- 55 Visible Human Resample
- 56 Visible Human Registration 1
For general information about installing SimpleITK please see the SimpleITK wiki.
Additionally the SPL's "Multi-modality MRI-based Atlas of the Brain" should be downloaded and extracted into the SimpleITK-Notebooks/Data directory.
http://www.spl.harvard.edu/publications/item/view/2037
For the Visible Human Notebooks the data should be downloaded from the MIDAS server.
http://midas3.kitware.com/midas/folder/10410
It is recommended to setup a separate Python virtual environment to run through these notebooks as a tutorial.
Under the best of circumstances (tested on OSX 10.8 and 10.7.5, RH6, Ubuntu 12) this environment can be setup with the following:
sudo pip install virtualenv
virtualenv ~/sitkpy --no-site-packages
~/sitkpy/bin/pip install ipython[all]
~/sitkpy/bin/pip install numpy
~/sitkpy/bin/pip install matplotlib
Note: On Linux platforms you may be able to obtain many of these packages as system packages which may suffice ( Ubuntu 12+). Note: On Window platforms some of these packages should be obtained as binary downloads and installed.
For many common platforms, a built distribution is available as an Python egg. This can be downloading and installed with the following command:
~/sitkpy/bin/easy_install SimpleITK
As of this writing, SimpleITK version >=0.6r1 is required to run these notebooks. This version currently needs to be downloaded from Source Forge
wxue: New Anaconda python distribution (early 2015) has includede SimpleITK in its package list. After install Anaconda, SimpleITK can be downloaded with the following command:
conda install --channel SimpleITK SimpleITK
More detailed process can be found:
http://www.cs.cmu.edu/~galeotti/methods_course/assignment-itkinstall.html
In this instruction, it recommends to install 32-bit Anaconda python in Windows machines.
To launch:
cd SimpleITK-Notebooks
~/sitkpy/bin/ipython notebook