scikit-image RAG Introduction

Humans possess an incredible ability to identify objects in an image. Image processing algorithms are still far behind this ability. Segmentation is the process of dividing an image into meaningful regions. All pixels belonging to a region should get a unique label in an ideal segmentation.

The current segmentation functions in scikit-image are too fine grained and fall closer to superpixel methods, providing a starting point for segmentation. Region Adjacency Graphs (RAGs) are a common data structure for many segmentation algorithms. As part of GSoC this year I am implementing RAGs for scikit-image. The current HEAD of scikit-image’s master branch contains my RAG implementation based on Networkx from my recent Pull Request. In the example below, we will see how Region Adjacency Graphs (RAGs) attempt to solve the segmentation problem.Please note that you need the latest master branch of scikit-image to run the following code.

Getting Started

We define the function show_img in preference to the standard call to imshow to set nice default size parameters.
We start with coffee, a nice fresh image of a coffee cup.

from skimage import graph, data, io, segmentation, color
from matplotlib import pyplot as plt
from skimage.measure import regionprops
from skimage import draw
import numpy as np

def show_img(img):
    width = 10.0
    height = img.shape[0]*width/img.shape[1]
    f = plt.figure(figsize=(width, height))

img =


Over Segmentation

We segment the image using SLIC algorithm. The SLIC algorithm will
assign a unique label to each region. This is a
localized cluster of pixels sharing some similar property, in this case their
color. The label of each pixel is stored in the labels array.

regionprops helps us compute various features of these regions. We will be
sing the centroid, purely for visualization.

labels = segmentation.slic(img, compactness=30, n_segments=400)
labels = labels + 1  # So that no labelled region is 0 and ignored by regionprops
regions = regionprops(labels)

The label2rgb function assigns a specific color to all pixels belonging to one
region (having the same label). In this case, in label_rgb each pixel is
replaces with the average RGB color of its region.

label_rgb = color.label2rgb(labels, img, kind='avg')

Just for clarity, we use mark_boundaries to highlight the region boundaries.
You will notice the the image is divided into more regions than required. This
phenomenon is called over-segmentation.

label_rgb = segmentation.mark_boundaries(label_rgb, labels, (0, 0, 0))


Enter, RAGs

Region Adjacency Graphs, as the name suggests represent adjacency of regions
with a graph. Each region in the image is a node in a graph. There is an edge
between every pair of adjacent regions (regions whose pixels are adjacent). The
weight of between every two nodes can be defined in a variety of ways. For this
example, we will use the difference of average color between two regions as
their edge weight. The more similar the regions, the lesser the weight between
them. Because we are using difference in mean color to compute the edge weight,
the method has been named rag_mean_color.

rag = graph.rag_mean_color(img, labels)

For our visualization, we are also adding an additional property to a node, the
coordinated of its centroid.

for region in regions:
    rag.node[region['label']]['centroid'] = region['centroid']

display_edges is a function to draw the edges of a RAG on its corresponding
image. It draws edges as green lines and centroids as yellow dots.
It also accepts an argument, thresh. We only draw edges with weight below this threshold.

def display_edges(image, g, threshold):
    """Draw edges of a RAG on its image

    Returns a modified image with the edges drawn.Edges are drawn in green
    and nodes are drawn in yellow.

    image : ndarray
        The image to be drawn on.
    g : RAG
        The Region Adjacency Graph.
    threshold : float
        Only edges in `g` below `threshold` are drawn.

    out: ndarray
        Image with the edges drawn.
    image = image.copy()
    for edge in g.edges_iter():
        n1, n2 = edge

        r1, c1 = map(int, rag.node[n1]['centroid'])
        r2, c2 = map(int, rag.node[n2]['centroid'])

        line  = draw.line(r1, c1, r2, c2)
        circle =,c1,2)

        if g[n1][n2]['weight'] < threshold :
            image[line] = 0,1,0
        image[circle] = 1,1,0

    return image

We call the function with thresh = infinity so that all edges are drawn. I
myself was surprised with the beauty of the following output.

edges_drawn_all = display_edges(label_rgb, rag, np.inf )


Let’s see what happens by setting thresh to 29, a value I arrived at with
some trial and error.

edges_drawn_29 = display_edges(label_rgb, rag, 29 )


Alas, the graph is cut

As you can see above, the RAG is now divided into disconnected regions. If you
notice, the table above and to the right of the dish is one big connected

Threshold Cut

The function cut_threshold removes edges below a specified threshold and then
labels a connected component as one region. Once the RAG is constructed, many similar
and more sophisticated strategies can improve the initial segmentation.

final_labels = graph.cut_threshold(labels, rag, 29)
final_label_rgb = color.label2rgb(final_labels, img, kind='avg')

Not perfect, but not that bad I’d say. My next steps will be to implement better algorithms to process the RAG after the initial segmentation.These include the merging predicates mention here and N-cut.


8 thoughts on “scikit-image RAG Introduction

  1. Pingback: Normalized Cuts on Region Adjacency Graphs | A Simple Progammer's Blog
  2. Pingback: A Simple Progammer's Blog
  3. Pingback: Hierarchical Merging of Region Adjacency Graphs | A Simple Progammer's Blog
  4. Pingback: GSoC 2014 – Signing off | A Simple Progammer's Blog

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