{"id":20215198,"url":"https://github.com/kitwaremedical/courseinbiomedicalimageanalysisandvisualization","last_synced_at":"2025-04-10T14:11:05.728Z","repository":{"id":138391595,"uuid":"173313156","full_name":"KitwareMedical/CourseInBiomedicalImageAnalysisAndVisualization","owner":"KitwareMedical","description":"Kitware Course in Biomedical Image Analysis and Visualization: ITK","archived":false,"fork":false,"pushed_at":"2025-01-03T16:14:29.000Z","size":40105,"stargazers_count":15,"open_issues_count":1,"forks_count":7,"subscribers_count":12,"default_branch":"master","last_synced_at":"2025-03-24T12:55:32.768Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://mybinder.org/v2/gh/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization/master","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KitwareMedical.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-03-01T14:13:09.000Z","updated_at":"2025-01-03T16:14:33.000Z","dependencies_parsed_at":null,"dependency_job_id":"bad57160-6f33-4a55-b03e-6e928033ad7c","html_url":"https://github.com/KitwareMedical/CourseInBiomedicalImageAnalysisAndVisualization","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KitwareMedical%2FCourseInBiomedicalImageAnalysisAndVisualization","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KitwareMedical%2FCourseInBiomedicalImageAnalysisAndVisualization/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KitwareMedical%2FCourseInBiomedicalImageAnalysisAndVisualization/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KitwareMedical%2FCourseInBiomedicalImageAnalysisAndVisualization/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KitwareMedical","download_url":"https://codeload.github.com/KitwareMedical/CourseInBiomedicalImageAnalysisAndVisualization/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248232418,"owners_count":21069487,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-14T06:20:23.382Z","updated_at":"2025-04-10T14:11:05.720Z","avatar_url":"https://github.com/KitwareMedical.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"**NOTE:** The updated version of this course material is here: https://github.com/InsightSoftwareConsortium/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse\n\nBiomedical Image Analysis and Visualization: ITK\n================================================\nKitware, Carrboro, North Carolina, USA\n======================================\n\n.. image:: https://mybinder.org/badge.svg\n  :target: https://mybinder.org/v2/gh/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization/master\n\nInstructors:\n\n- Matt McCormick, PhD\n- Dženan Zukić, PhD\n- Francois Budin\n\n.. image:: data/kitware-logo.png\n  :alt: Kitware\n  :width: 400px\n\n.. image:: data/itk-logo.png\n  :alt: ITK\n  :width: 500px\n\n\nThe `Insight Toolkit (ITK) (www.itk.org) \u003chttps://www.itk.org\u003e`_\nhas become a standard in academia and industry for\nmedical image analysis. In recent years, the ITK community has\nfocused on providing programming interfaces to ITK from Python and JavaScript\nand making ITK available via leading applications such as Slicer and ImageJ.\nIn this course we present best practices for taking advantage of ITK in your\nimaging research and commercial products. We demonstrate how script writing\nand can be used to access the algorithms in ITK and the\nmultitude of ITK extensions that are freely available on the web.\n\nRun the Tutorial\n----------------\n\nThere are many ways to run these tutorials.\n\nOn the Web, with Binder\n^^^^^^^^^^^^^^^^^^^^^^^\n\nTo run the notebooks in\n`MyBinder \u003chttps://mybinder.readthedocs.io/en/latest/\u003e`_,\nsimply `click this link \u003chttps://mybinder.org/v2/gh/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization/master\u003e`_.\n\nLocally, with Python from Python.org or a System Python\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFirst, `install Python\n\u003chttps://www.python.org/downloads/release/python-365/\u003e`_,\nif not already available.\n\nNext, install the required dependencies::\n\n   python -m pip install tornado==5.1.1 jupyter matplotlib numpy scipy ipywidgets scikit-learn cookiecutter\n   python -m pip install --upgrade --pre itk itk-texturefeatures\n   python -m pip install itkwidgets\n\nThen, clone the repository::\n\n  git clone https://github.com/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization.git\n  cd 2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization\n\nAnd start Jupyter::\n\n  python -m jupyter notebook\n\nLocally, with Conda\n^^^^^^^^^^^^^^^^^^^\n\nFirst, `install MiniConda \u003chttps://conda.io/miniconda.html\u003e`_ or Anaconda, if\nnot already available.\n\nNext, install the required dependencies::\n\n   conda install -c conda-forge jupyter matplotlib numpy scipy ipywidgets scikit-learn cookiecutter\n   python -m pip install --upgrade --pre itk itk-texturefeatures\n   python -m pip install itkwidgets\n\nThen, clone the repository::\n\n  git clone https://github.com/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization.git\n  cd 2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization\n\nAnd start Jupyter::\n\n  python -m jupyter notebook\n\nLocally, with Docker\n^^^^^^^^^^^^^^^^^^^^\n\nFirst, `install Docker \u003chttps://docs.docker.com/install/\u003e`_, if not already\navailable.\n\nNext, clone the repository::\n\n  git clone https://github.com/KitwareMedical/2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization.git\n  cd 2019-03-13-KRSCourseInBiomedicalImageAnalysisAndVisualization\n\nThen, build and run the Docker image::\n\n  ./build.sh\n  ./run.sh\n\nPaste the URL presented in the terminal in your web browser.\n\nWith Jupyter Lab instead of the Jupyter Notebook\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nTo run under [Jupyter Lab](https://jupyterlab.readthedocs.io/en/stable/)\ninstead of the Jupyter Notebook, install the *jupyterlab* package and\n[Node.js](https://nodejs.org/en/download/), e.g.::\n\n  conda install jupyterlab nodejs\n\nThen install the required extensions::\n\n  jupyter labextension install @jupyter-widgets/jupyterlab-manager itk-jupyter-widgets\n\nAnd start Jupyter with::\n\n  python -m jupyter lab\n\ninstead of::\n\n  python -m jupyter notebook\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkitwaremedical%2Fcourseinbiomedicalimageanalysisandvisualization","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkitwaremedical%2Fcourseinbiomedicalimageanalysisandvisualization","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkitwaremedical%2Fcourseinbiomedicalimageanalysisandvisualization/lists"}