Jupyter widgets to visualize images in 2D and 3D
Project description
itk-jupyter-widgets
===================
.. image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
:target: https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/LICENSE
:alt: License
.. image:: https://img.shields.io/pypi/v/itkwidgets.svg
:target: https://pypi-hypernode.com/pypi/itkwidgets
:alt: PyPI
.. image:: https://circleci.com/gh/InsightSoftwareConsortium/itk-jupyter-widgets.svg?style=shield
:target: https://circleci.com/gh/InsightSoftwareConsortium/itk-jupyter-widgets
:alt: Build status
.. image:: https://mybinder.org/badge.svg
:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F3DImage.ipynb
Interactive `Jupyter <https://jupyter.org/>`_ widgets to visualize images in 2D and 3D.
.. image:: https://i.imgur.com/d8aXycW.png
:width: 800px
:alt: itk-jupyter-widgets chest CT in JupyterLab
These widgets are designed to support image analysis with the `Insight Toolkit
(ITK) <https://itk.org/>`_, but they also work with other spatial analysis tools
in the scientific Python ecosystem.
These widgets are built on
`itk.js <https://github.com/InsightSoftwareConsortium/itk-js>`_ and
`vtk.js <https://github.com/Kitware/vtk-js>`_.
.. image:: https://thumbs.gfycat.com/ShyFelineBeetle-size_restricted.gif
:width: 640px
:alt: itk-jupyter-widgets demo
:align: center
Installation
------------
To install the widgets for the Jupyter Notebook::
pip install itkwidgets
For Jupyter Lab, additionally run::
jupyter labextension install @jupyter-widgets/jupyterlab-manager itk-jupyter-widgets
Examples
--------
After installation, try the following examples that demonstrate how to visualize:
- `2D ITK Images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/2DImage.ipynb>`_
- `3D ITK Images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/3DImage.ipynb>`_
- `Dask Array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/DaskArray.ipynb>`_
- `ImageJ ImgLib2 images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/ImageJImgLib2.ipynb>`_ (requires `conda <https://conda.io/>`_ and a local `Fiji <https://fiji.sc/>`_ installation)
- `NumPy array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/NumPyArray.ipynb>`_ (processed with SciPy)
- `NumPy array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/scikit-image.ipynb>`_ (processed with scikit-image)
- `VTK vtkImageData <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/vtkImageData.ipynb>`_
or how to:
- `Select a region of interest <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/SelectRegionOfInterest.ipynb>`_
- `Specify a colormap <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/SpecifyAColormap.ipynb>`_
Examples on Binder
--------
- `2D ITK Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F2DImage.ipynb>`_
- `3D ITK Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F3DImage.ipynb>`_
- `Dask Array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/DaskArray.ipynb>`_
- `NumPy array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/NumPyArray.ipynb>`_ (processed with SciPy)
- `NumPy array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/scikit-image.ipynb>`_ (processed with scikit-image)
- `Select a region of interest <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/SelectRegionOfInterest.ipynb>`_
- `Specify a colormap <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/SpecifyAColormap.ipynb>`_
Troubleshooting
---------------
If you experience the notebook warning::
IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--NotebookApp.iopub_data_rate_limit`.
Set the notebook configuration value::
jupyter notebook --NotebookApp.iopub_data_rate_limit=1e12
Hacking
-------
For a development installation (requires `Node.js <https://nodejs.org/en/download/>`_)::
git clone https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets.git
cd itk-jupyter-widgets
python -m pip install -r requirements-dev.txt -r requirements.txt
python -m pip install -e .
jupyter nbextension install --py --symlink --sys-prefix itkwidgets
jupyter nbextension enable --py --sys-prefix itkwidgets
jupyter nbextension enable --py --sys-prefix widgetsnbextension
python -m pytest
The above commands will setup your system for development with the Jupyter
Notebook. To develop for Jupyter Lab, additionally run::
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter labextension install ./js
.. warning::
This project is under active development. Its API and behavior may change at
any time. We mean it.
===================
.. image:: https://img.shields.io/badge/License-Apache%202.0-blue.svg
:target: https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/LICENSE
:alt: License
.. image:: https://img.shields.io/pypi/v/itkwidgets.svg
:target: https://pypi-hypernode.com/pypi/itkwidgets
:alt: PyPI
.. image:: https://circleci.com/gh/InsightSoftwareConsortium/itk-jupyter-widgets.svg?style=shield
:target: https://circleci.com/gh/InsightSoftwareConsortium/itk-jupyter-widgets
:alt: Build status
.. image:: https://mybinder.org/badge.svg
:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F3DImage.ipynb
Interactive `Jupyter <https://jupyter.org/>`_ widgets to visualize images in 2D and 3D.
.. image:: https://i.imgur.com/d8aXycW.png
:width: 800px
:alt: itk-jupyter-widgets chest CT in JupyterLab
These widgets are designed to support image analysis with the `Insight Toolkit
(ITK) <https://itk.org/>`_, but they also work with other spatial analysis tools
in the scientific Python ecosystem.
These widgets are built on
`itk.js <https://github.com/InsightSoftwareConsortium/itk-js>`_ and
`vtk.js <https://github.com/Kitware/vtk-js>`_.
.. image:: https://thumbs.gfycat.com/ShyFelineBeetle-size_restricted.gif
:width: 640px
:alt: itk-jupyter-widgets demo
:align: center
Installation
------------
To install the widgets for the Jupyter Notebook::
pip install itkwidgets
For Jupyter Lab, additionally run::
jupyter labextension install @jupyter-widgets/jupyterlab-manager itk-jupyter-widgets
Examples
--------
After installation, try the following examples that demonstrate how to visualize:
- `2D ITK Images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/2DImage.ipynb>`_
- `3D ITK Images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/3DImage.ipynb>`_
- `Dask Array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/DaskArray.ipynb>`_
- `ImageJ ImgLib2 images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/ImageJImgLib2.ipynb>`_ (requires `conda <https://conda.io/>`_ and a local `Fiji <https://fiji.sc/>`_ installation)
- `NumPy array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/NumPyArray.ipynb>`_ (processed with SciPy)
- `NumPy array images <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/scikit-image.ipynb>`_ (processed with scikit-image)
- `VTK vtkImageData <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/vtkImageData.ipynb>`_
or how to:
- `Select a region of interest <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/SelectRegionOfInterest.ipynb>`_
- `Specify a colormap <https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets/blob/master/examples/SpecifyAColormap.ipynb>`_
Examples on Binder
--------
- `2D ITK Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F2DImage.ipynb>`_
- `3D ITK Images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F3DImage.ipynb>`_
- `Dask Array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/DaskArray.ipynb>`_
- `NumPy array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/NumPyArray.ipynb>`_ (processed with SciPy)
- `NumPy array images <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/scikit-image.ipynb>`_ (processed with scikit-image)
- `Select a region of interest <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/SelectRegionOfInterest.ipynb>`_
- `Specify a colormap <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/SpecifyAColormap.ipynb>`_
Troubleshooting
---------------
If you experience the notebook warning::
IOPub data rate exceeded.
The notebook server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--NotebookApp.iopub_data_rate_limit`.
Set the notebook configuration value::
jupyter notebook --NotebookApp.iopub_data_rate_limit=1e12
Hacking
-------
For a development installation (requires `Node.js <https://nodejs.org/en/download/>`_)::
git clone https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets.git
cd itk-jupyter-widgets
python -m pip install -r requirements-dev.txt -r requirements.txt
python -m pip install -e .
jupyter nbextension install --py --symlink --sys-prefix itkwidgets
jupyter nbextension enable --py --sys-prefix itkwidgets
jupyter nbextension enable --py --sys-prefix widgetsnbextension
python -m pytest
The above commands will setup your system for development with the Jupyter
Notebook. To develop for Jupyter Lab, additionally run::
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter labextension install ./js
.. warning::
This project is under active development. Its API and behavior may change at
any time. We mean it.
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