with interactive scientific computing in the SciPy ecosystem
IPython 0.7.2 released June 6, 2006
[Image source](https://en.wikipedia.org/wiki/IPython)IPython 0.12.0 released December 18, 2011
[Image source](http://pgbovine.net/ipython-notebook-first-impressions.htm)Fernando announces Project Jupyter at SciPy 2014
[Image source](https://jupyter.org/)"JupyterLab is Ready for Users" - February 20, 2018
[Image source](https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906)"To start developing a JupyterLab extension, see the JupyterLab Extension Developer Guide and the TypeScript or JavaScript extension templates. JupyterLab itself is co-developed on top of PhosphorJS, a new Javascript library for building extensible, high-performance, desktop-style web applications. We use modern JavaScript technologies such as TypeScript, React, Lerna, Yarn, and webpack."
Interactive visualization to support multi-dimensional spatial analysis
A Jupyter / Leaflet bridge enabling interactive maps in the Jupyter notebook.
GeoNotebook is an application that provides client/server environment with interactive visualization and analysis capabilities using Jupyter, GeoJS and other open source tools.
3d plotting for Python in the Jupyter notebook based on IPython widgets using WebGL.
These widgets are designed to support spatial analysis with the Insight Toolkit (ITK), but they also work with other spatial analysis tools in the scientific Python ecosystem.
from itkwidgets import view
import itk
PixelType = itk.ctype('float')
image = itk.imread(brainFileName, PixelType)
view(image)
Failed to display Jupyter Widget of type Viewer
.
If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean that the widgets JavaScript is still loading. If this message persists, it likely means that the widgets JavaScript library is either not installed or not enabled. See the Jupyter Widgets Documentation for setup instructions.
If you're reading this message in another frontend (for example, a static rendering on GitHub or NBViewer), it may mean that your frontend doesn't currently support widgets.
# Smooth the image
smoother = itk.CurvatureFlowImageFilter.New(image)
smoother.SetNumberOfIterations(6)
smoother.SetTimeStep(0.05)
smoother.Update()
view(smoother.GetOutput())
Failed to display Jupyter Widget of type Viewer
.
If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean that the widgets JavaScript is still loading. If this message persists, it likely means that the widgets JavaScript library is either not installed or not enabled. See the Jupyter Widgets Documentation for setup instructions.
If you're reading this message in another frontend (for example, a static rendering on GitHub or NBViewer), it may mean that your frontend doesn't currently support widgets.
confidence_connected = itk.ConfidenceConnectedImageFilter.New(smoother.GetOutput())
confidence_connected.SetMultiplier(2.5)
confidence_connected.SetNumberOfIterations(5)
confidence_connected.SetInitialNeighborhoodRadius(2)
confidence_connected.SetReplaceValue(255)
Dimension = image.GetImageDimension()
SeedType = itk.Index[Dimension]
seed1 = SeedType()
seed1[0] = 118
seed1[1] = 133
seed1[2] = 92
confidence_connected.AddSeed(seed1)
seed2 = SeedType()
seed2[0] = 63
seed2[1] = 135
seed2[2] = 94
confidence_connected.AddSeed(seed2)
seed3 = SeedType()
seed3[0] = 63
seed3[1] = 157
seed3[2] = 90
confidence_connected.AddSeed(seed3)
seed4 = SeedType()
seed4[0] = 111
seed4[1] = 150
seed4[2] = 90
confidence_connected.AddSeed(seed4)
seed5 = SeedType()
seed5[0] = 111
seed5[1] = 50
seed5[2] = 88
confidence_connected.AddSeed(seed5)
confidence_connected.Update()
view(confidence_connected.GetOutput())
Failed to display Jupyter Widget of type Viewer
.
If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean that the widgets JavaScript is still loading. If this message persists, it likely means that the widgets JavaScript library is either not installed or not enabled. See the Jupyter Widgets Documentation for setup instructions.
If you're reading this message in another frontend (for example, a static rendering on GitHub or NBViewer), it may mean that your frontend doesn't currently support widgets.
American Heart Association, Precision Medicine Platform
[Image source](https://precision.heart.org/workspace)Email: matt.mccormick@kitware.com