.. _sphx_glr_auto_examples_segmentation:

Segmentation of objects
-----------------------



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    <div class="sphx-glr-thumbnails">


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    <div class="sphx-glr-thumbcontainer" tooltip="Construct a region boundary RAG with the rag_boundary function. The function  :pyskimage.graph....">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_rag_boundary_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_rag_boundary.py`

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      <div class="sphx-glr-thumbnail-title">Region Boundary based RAGs</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example constructs a Region Adjacency Graph (RAG) and merges regions which are similar in ...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_rag_mean_color_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_rag_mean_color.py`

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      <div class="sphx-glr-thumbnail-title">RAG Thresholding</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example constructs a Region Adjacency Graph (RAG) and recursively performs a Normalized Cu...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_ncut_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_ncut.py`

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      <div class="sphx-glr-thumbnail-title">Normalized Cut</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The watershed transform is commonly used as a starting point for many segmentation algorithms. ...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_compact_watershed_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_compact_watershed.py`

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      <div class="sphx-glr-thumbnail-title">Find Regular Segments Using Compact Watershed</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Thresholding is used to create a binary image from a grayscale image [1]_.">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_thresholding_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_thresholding.py`

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      <div class="sphx-glr-thumbnail-title">Thresholding</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example constructs a Region Adjacency Graph (RAG) and draws it with the rag_draw method.">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_rag_draw_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_rag_draw.py`

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      <div class="sphx-glr-thumbnail-title">Drawing Region Adjacency Graphs (RAGs)</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The Chan-Vese segmentation algorithm is designed to segment objects without clearly defined bou...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_chan_vese_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_chan_vese.py`

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      <div class="sphx-glr-thumbnail-title">Chan-Vese Segmentation</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The peak_local_max function returns the coordinates of local peaks (maxima) in an image. Intern...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_peak_local_max_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_peak_local_max.py`

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      <div class="sphx-glr-thumbnail-title">Finding local maxima</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Niblack and Sauvola thresholds are local thresholding techniques that are useful for images whe...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_niblack_sauvola_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_niblack_sauvola.py`

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      <div class="sphx-glr-thumbnail-title">Niblack and Sauvola Thresholding</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The multi-Otsu threshold [1]_ is a thresholding algorithm that is used to separate the pixels o...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_multiotsu_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_multiotsu.py`

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      <div class="sphx-glr-thumbnail-title">Multi-Otsu Thresholding</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example is about comparing the segmentations obtained using the plain SLIC method [1]_ and...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_mask_slic_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_mask_slic.py`

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      <div class="sphx-glr-thumbnail-title">Apply maskSLIC vs SLIC</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The random walker algorithm [1]_  determines the segmentation of an image from a set of markers...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_random_walker_segmentation_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_random_walker_segmentation.py`

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      <div class="sphx-glr-thumbnail-title">Random walker segmentation</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Given several connected components represented by a label image, these connected components can...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_expand_labels_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_expand_labels.py`

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      <div class="sphx-glr-thumbnail-title">Expand segmentation labels without overlap</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The watershed is a classical algorithm used for segmentation, that is, for separating different...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_watershed_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_watershed.py`

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      <div class="sphx-glr-thumbnail-title">Watershed segmentation</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to segment an image with image labelling. The following steps are applie...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_label_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_label.py`

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      <div class="sphx-glr-thumbnail-title">Label image regions</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The watershed is a classical algorithm used for segmentation, that is, for separating different...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_marked_watershed_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_marked_watershed.py`

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      <div class="sphx-glr-thumbnail-title">Markers for watershed transform</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example compares four popular low-level image segmentation methods.  As it is difficult to...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_segmentations_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_segmentations.py`

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      <div class="sphx-glr-thumbnail-title">Comparison of segmentation and superpixel algorithms</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="When segmenting an image, you may want to combine multiple alternative segmentations. The :pysk...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_join_segmentations_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_join_segmentations.py`

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      <div class="sphx-glr-thumbnail-title">Find the intersection of two segmentations</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates the use of the merge_nodes function of a Region Adjacency Graph (RAG)...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_rag_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_rag.py`

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      <div class="sphx-glr-thumbnail-title">Region Adjacency Graphs</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we show the error on measuring perimeters, comparing classic approximations an...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_perimeters_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_perimeters.py`

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      <div class="sphx-glr-thumbnail-title">Measure perimeters with different estimators</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example constructs a Region Adjacency Graph (RAG) and progressively merges regions that ar...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_rag_merge_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_rag_merge.py`

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      <div class="sphx-glr-thumbnail-title">RAG Merging</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to perform hierarchical merging on region boundary Region Adjacen...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_boundary_merge_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_boundary_merge.py`

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      <div class="sphx-glr-thumbnail-title">Hierarchical Merging of Region Boundary RAGs</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="We detect local maxima in a galaxy image. The image is corrupted by noise, generating many loca...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_extrema_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_extrema.py`

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      <div class="sphx-glr-thumbnail-title">Extrema</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This toy example shows how to compute the size of every labelled region in a series of 10 image...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_regionprops_table_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_regionprops_table.py`

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      <div class="sphx-glr-thumbnail-title">Explore and visualize region properties with pandas</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to calculate the Hausdorff distance between two sets of points. The Haus...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_hausdorff_distance_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_hausdorff_distance.py`

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      <div class="sphx-glr-thumbnail-title">Hausdorff Distance</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to measure properties of labelled image regions. We first analyze an ima...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_regionprops_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_regionprops.py`

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      <div class="sphx-glr-thumbnail-title">Measure region properties</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="A pixel-based segmentation is computed here using local features based on local intensity, edge...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_trainable_segmentation_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_trainable_segmentation.py`

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      <div class="sphx-glr-thumbnail-title">Trainable segmentation using local features and random forests</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Morphological Snakes [1]_ are a family of methods for image segmentation. Their behavior is sim...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_morphsnakes_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_morphsnakes.py`

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      <div class="sphx-glr-thumbnail-title">Morphological Snakes</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Flood fill is an algorithm to identify and/or change adjacent values in an image based on their...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_floodfill_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_floodfill.py`

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      <div class="sphx-glr-thumbnail-title">Flood Fill</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows an illustration of the computation of the Euler number [1]_ in 2D and 3D obj...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_euler_number_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_euler_number.py`

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      <div class="sphx-glr-thumbnail-title">Euler number</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="When trying out different segmentation methods, how do you know which one is best? If you have ...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_metrics_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_metrics.py`

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      <div class="sphx-glr-thumbnail-title">Evaluating segmentation metrics</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The rolling-ball algorithm estimates the background intensity of a grayscale image in case of u...">

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  .. image:: /auto_examples/segmentation/images/thumb/sphx_glr_plot_rolling_ball_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_segmentation_plot_rolling_ball.py`

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      <div class="sphx-glr-thumbnail-title">Use rolling-ball algorithm for estimating background intensity</div>
    </div>


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    </div>


.. toctree::
   :hidden:

   /auto_examples/segmentation/plot_rag_boundary
   /auto_examples/segmentation/plot_rag_mean_color
   /auto_examples/segmentation/plot_ncut
   /auto_examples/segmentation/plot_compact_watershed
   /auto_examples/segmentation/plot_thresholding
   /auto_examples/segmentation/plot_rag_draw
   /auto_examples/segmentation/plot_chan_vese
   /auto_examples/segmentation/plot_peak_local_max
   /auto_examples/segmentation/plot_niblack_sauvola
   /auto_examples/segmentation/plot_multiotsu
   /auto_examples/segmentation/plot_mask_slic
   /auto_examples/segmentation/plot_random_walker_segmentation
   /auto_examples/segmentation/plot_expand_labels
   /auto_examples/segmentation/plot_watershed
   /auto_examples/segmentation/plot_label
   /auto_examples/segmentation/plot_marked_watershed
   /auto_examples/segmentation/plot_segmentations
   /auto_examples/segmentation/plot_join_segmentations
   /auto_examples/segmentation/plot_rag
   /auto_examples/segmentation/plot_perimeters
   /auto_examples/segmentation/plot_rag_merge
   /auto_examples/segmentation/plot_boundary_merge
   /auto_examples/segmentation/plot_extrema
   /auto_examples/segmentation/plot_regionprops_table
   /auto_examples/segmentation/plot_hausdorff_distance
   /auto_examples/segmentation/plot_regionprops
   /auto_examples/segmentation/plot_trainable_segmentation
   /auto_examples/segmentation/plot_morphsnakes
   /auto_examples/segmentation/plot_floodfill
   /auto_examples/segmentation/plot_euler_number
   /auto_examples/segmentation/plot_metrics
   /auto_examples/segmentation/plot_rolling_ball