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import itk
from packaging.version import parse
from importlib.metadata import version
if parse(version('itk')) < parse('5.3'):
raise ValueError("ITK greater than version 5.3.0 is required for this notebook")
from itkwidgets import view
file_name = "data/brainweb165a10f17.mha"
image = itk.imread(file_name, itk.ctype("float"))
view(image, gradient_opacity=0.5)
<itkwidgets.viewer.Viewer at 0x7fa2755add10>
# Smooth the image
smoothed = itk.curvature_flow_image_filter(
image, number_of_iterations=6, time_step=0.005
)
view(smoothed, gradient_opacity=0.5)
<itkwidgets.viewer.Viewer at 0x7fa2733fe010>
# Segment the white matter with a 3D region-growing algorithm
confidence_connected = itk.ConfidenceConnectedImageFilter.New(smoothed)
confidence_connected.SetMultiplier(2.5)
confidence_connected.SetNumberOfIterations(5)
confidence_connected.SetInitialNeighborhoodRadius(2)
confidence_connected.SetReplaceValue(255)
confidence_connected.AddSeed([118, 133, 92])
confidence_connected.AddSeed([63, 135, 94])
confidence_connected.AddSeed([63, 157, 90])
confidence_connected.AddSeed([111, 150, 90])
confidence_connected.AddSeed([111, 50, 88])
confidence_connected.Update()
view(
image=smoothed,
label_image=confidence_connected.GetOutput(),
gradient_opacity=0.5
)
<itkwidgets.viewer.Viewer at 0x7fa2755ad4d0>
In 1999, the US National Institute of Health’s (NIH) National Library of Medicine (NLM) started a project to support the Visible Human Project.
ITK contributors locations for the 4.8 and 4.9 releases.
ITK Software Guide: https://www.itk.org/ItkSoftwareGuide.pdf
Discourse Discussion: https://discourse.itk.org
Sphinx Examples: https://www.itk.org/ITKExamples
ITK/Examples/
directory in the ITK source code repository
Kitware: https://www.kitware.com/