https://github.com/kitwaremedical/courseinbiomedicalimageanalysisandvisualization
Kitware Course in Biomedical Image Analysis and Visualization: ITK
https://github.com/kitwaremedical/courseinbiomedicalimageanalysisandvisualization
Last synced: about 1 year ago
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Kitware Course in Biomedical Image Analysis and Visualization: ITK
- Host: GitHub
- URL: https://github.com/kitwaremedical/courseinbiomedicalimageanalysisandvisualization
- Owner: KitwareMedical
- License: apache-2.0
- Created: 2019-03-01T14:13:09.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2025-01-03T16:14:29.000Z (over 1 year ago)
- Last Synced: 2025-03-24T12:55:32.768Z (over 1 year ago)
- Language: Jupyter Notebook
- Homepage: https://mybinder.org/v2/gh/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization/master
- Size: 38.2 MB
- Stars: 15
- Watchers: 12
- Forks: 7
- Open Issues: 1
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
**NOTE:** The updated version of this course material is here: https://github.com/InsightSoftwareConsortium/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse
Biomedical Image Analysis and Visualization: ITK
================================================
Kitware, Carrboro, North Carolina, USA
======================================
.. image:: https://mybinder.org/badge.svg
:target: https://mybinder.org/v2/gh/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization/master
Instructors:
- Matt McCormick, PhD
- Dženan Zukić, PhD
- Francois Budin
.. image:: data/kitware-logo.png
:alt: Kitware
:width: 400px
.. image:: data/itk-logo.png
:alt: ITK
:width: 500px
The `Insight Toolkit (ITK) (www.itk.org) `_
has become a standard in academia and industry for
medical image analysis. In recent years, the ITK community has
focused on providing programming interfaces to ITK from Python and JavaScript
and making ITK available via leading applications such as Slicer and ImageJ.
In this course we present best practices for taking advantage of ITK in your
imaging research and commercial products. We demonstrate how script writing
and can be used to access the algorithms in ITK and the
multitude of ITK extensions that are freely available on the web.
Run the Tutorial
----------------
There are many ways to run these tutorials.
On the Web, with Binder
^^^^^^^^^^^^^^^^^^^^^^^
To run the notebooks in
`MyBinder `_,
simply `click this link `_.
Locally, with Python from Python.org or a System Python
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
First, `install Python
`_,
if not already available.
Next, install the required dependencies::
python -m pip install tornado==5.1.1 jupyter matplotlib numpy scipy ipywidgets scikit-learn cookiecutter
python -m pip install --upgrade --pre itk itk-texturefeatures
python -m pip install itkwidgets
Then, clone the repository::
git clone https://github.com/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization.git
cd 2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization
And start Jupyter::
python -m jupyter notebook
Locally, with Conda
^^^^^^^^^^^^^^^^^^^
First, `install MiniConda `_ or Anaconda, if
not already available.
Next, install the required dependencies::
conda install -c conda-forge jupyter matplotlib numpy scipy ipywidgets scikit-learn cookiecutter
python -m pip install --upgrade --pre itk itk-texturefeatures
python -m pip install itkwidgets
Then, clone the repository::
git clone https://github.com/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization.git
cd 2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization
And start Jupyter::
python -m jupyter notebook
Locally, with Docker
^^^^^^^^^^^^^^^^^^^^
First, `install Docker `_, if not already
available.
Next, clone the repository::
git clone https://github.com/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization.git
cd 2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization
Then, build and run the Docker image::
./build.sh
./run.sh
Paste the URL presented in the terminal in your web browser.
With Jupyter Lab instead of the Jupyter Notebook
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
To run under [Jupyter Lab](https://jupyterlab.readthedocs.io/en/stable/)
instead of the Jupyter Notebook, install the *jupyterlab* package and
[Node.js](https://nodejs.org/en/download/), e.g.::
conda install jupyterlab nodejs
Then install the required extensions::
jupyter labextension install @jupyter-widgets/jupyterlab-manager itk-jupyter-widgets
And start Jupyter with::
python -m jupyter lab
instead of::
python -m jupyter notebook