Define Content of Interest with Image Masks¶

Often, some content in the images may not correspond. For example, there may be background content or noisy areas. A mask defined on the fixed and/or moving image can be used to exclude these regions at a pixel level from the similarity metric computations. This improves the robustness of registration.

For more information, see Section 5.4, "Masks" of the Elastix Manual.

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import itk
from itkwidgets import view, compare

In [26]:

# Lung SEM slices
# Grothausmann, R., Knudsen, L., Ochs, M., and Mühlfeld, C.: Digital 3D reconstructions
# using histological serial sections of lung tissue including the alveolar
# capillary network. American Journal of Physiology - Lung Cellular and Molecular
# Physiology 312(2), L243–L257 (2017). doi: 10.1152/ajplung.00326.2016
fixed = itk.imread('data/lung_sem/2016_12_02_0101_s00_01.png', itk.F)
moving = itk.imread('data/lung_sem/2016_12_02_0101_s00_02.png', itk.F)

There are inconsistent dirt particles in each slice. Let's exclude these with a mask.

In [24]:

compare(fixed, moving, ui_collapsed=True)

AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…

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MaskImageType = itk.Image[itk.UC, 2]
fixed_mask = itk.binary_threshold_image_filter(fixed,
                                               lower_threshold=80.0,
                                               inside_value=1,
                                               ttype=(type(fixed), MaskImageType))
compare(fixed, fixed_mask)

AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…

In [33]:

moving_mask = itk.binary_threshold_image_filter(moving,
                                                lower_threshold=80.0,
                                                inside_value=1,
                                                ttype=(type(moving), MaskImageType))
compare(moving, moving_mask)

AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…

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parameters = itk.ParameterObject.New()
parameters.ReadParameterFile('data/lung_sem/ParameterFile.txt')

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registered = itk.elastix_registration_method(fixed, moving,
                                             parameter_object=parameters,
                                             fixed_mask=fixed_mask, moving_mask=moving_mask)

In [45]:

compare(fixed, registered, ui_collapsed=True)

AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…