Jupyter widgets to visualize images in 2D and 3D
Project description
Interactive Jupyter widgets to visualize images in 2D and 3D.
These widgets are designed to support image analysis with the Insight Toolkit (ITK), but they also work with other spatial analysis tools in the scientific Python ecosystem.
These widgets are built on itk.js and vtk.js.
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:
ImageJ ImgLib2 images (requires conda and a local Fiji installation)
or how to:
Examples on Binder
Data types:
Tasks:
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):
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
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