.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/segmentation/plot_mask_slic.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_segmentation_plot_mask_slic.py>`
        to download the full example code or to run this example in your browser via Binder

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_segmentation_plot_mask_slic.py:


======================
Apply maskSLIC vs SLIC
======================

This example is about comparing the segmentations obtained using the
plain SLIC method [1]_ and its masked version maskSLIC [2]_.

To illustrate these segmentation methods, we use an image of biological tissue
with immunohistochemical (IHC) staining. The same biomedical image is used in
the example on how to
:ref:`sphx_glr_auto_examples_color_exposure_plot_ihc_color_separation.py`.

The maskSLIC method is an extension of the SLIC method for the
generation of superpixels in a region of interest. maskSLIC is able to
overcome border problems that affects SLIC method, particularely in
case of irregular mask.

.. [1] Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi,
    Pascal Fua, and Sabine Süsstrunk, "SLIC Superpixels Compared to
    State-of-the-Art Superpixel Methods," IEEE TPAMI, 2012,
    :DOI:`10.1109/TPAMI.2012.120`

.. [2] Irving, Benjamin. "maskSLIC: regional superpixel generation
    with application to local pathology characterisation in medical
    images," 2016, :arXiv:`1606.09518`

.. GENERATED FROM PYTHON SOURCE LINES 29-77



.. image-sg:: /auto_examples/segmentation/images/sphx_glr_plot_mask_slic_001.png
   :alt: Original image, Mask, SLIC, maskSLIC
   :srcset: /auto_examples/segmentation/images/sphx_glr_plot_mask_slic_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    import matplotlib.pyplot as plt

    from skimage import data
    from skimage import color
    from skimage import morphology
    from skimage import segmentation

    # Input data
    img = data.immunohistochemistry()

    # Compute a mask
    lum = color.rgb2gray(img)
    mask = morphology.remove_small_holes(
        morphology.remove_small_objects(lum < 0.7, 500), 500
    )

    mask = morphology.opening(mask, morphology.disk(3))

    # SLIC result
    slic = segmentation.slic(img, n_segments=200, start_label=1)

    # maskSLIC result
    m_slic = segmentation.slic(img, n_segments=100, mask=mask, start_label=1)

    # Display result
    fig, ax_arr = plt.subplots(2, 2, sharex=True, sharey=True, figsize=(10, 10))
    ax1, ax2, ax3, ax4 = ax_arr.ravel()

    ax1.imshow(img)
    ax1.set_title('Original image')

    ax2.imshow(mask, cmap='gray')
    ax2.set_title('Mask')

    ax3.imshow(segmentation.mark_boundaries(img, slic))
    ax3.contour(mask, colors='red', linewidths=1)
    ax3.set_title('SLIC')

    ax4.imshow(segmentation.mark_boundaries(img, m_slic))
    ax4.contour(mask, colors='red', linewidths=1)
    ax4.set_title('maskSLIC')

    for ax in ax_arr.ravel():
        ax.set_axis_off()

    plt.tight_layout()
    plt.show()


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 1.665 seconds)


.. _sphx_glr_download_auto_examples_segmentation_plot_mask_slic.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: binder-badge

      .. image:: images/binder_badge_logo.svg
        :target: https://mybinder.org/v2/gh/scikit-image/scikit-image/v0.23.2?filepath=notebooks/auto_examples/segmentation/plot_mask_slic.ipynb
        :alt: Launch binder
        :width: 150 px

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_mask_slic.ipynb <plot_mask_slic.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_mask_slic.py <plot_mask_slic.py>`


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 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_