segmentation
¶skimage.segmentation.random_walker (data, labels) 
Random walker algorithm for segmentation from markers. 
skimage.segmentation.active_contour (image, snake) 
Active contour model. 
skimage.segmentation.felzenszwalb (image[, …]) 
Computes Felsenszwalb’s efficient graph based image segmentation. 
skimage.segmentation.slic (image[, …]) 
Segments image using kmeans clustering in Color(x,y,z) space. 
skimage.segmentation.quickshift (image[, …]) 
Segments image using quickshift clustering in Color(x,y) space. 
skimage.segmentation.find_boundaries (label_img) 
Return bool array where boundaries between labeled regions are True. 
skimage.segmentation.mark_boundaries (image, …) 
Return image with boundaries between labeled regions highlighted. 
skimage.segmentation.clear_border (labels[, …]) 
Clear objects connected to the label image border. 
skimage.segmentation.join_segmentations (s1, s2) 
Return the join of the two input segmentations. 
skimage.segmentation.relabel_from_one (…) 
Deprecated function. 
skimage.segmentation.relabel_sequential (…) 
Relabel arbitrary labels to {offset, … 
skimage.segmentation.watershed (image, markers) 
Find watershed basins in image flooded from given markers. 
skimage.segmentation.chan_vese (image[, mu, …]) 
ChanVese segmentation algorithm. 
skimage.segmentation.morphological_geodesic_active_contour (…) 
Morphological Geodesic Active Contours (MorphGAC). 
skimage.segmentation.morphological_chan_vese (…) 
Morphological Active Contours without Edges (MorphACWE) 
skimage.segmentation.inverse_gaussian_gradient (image) 
Inverse of gradient magnitude. 
skimage.segmentation.circle_level_set (…[, …]) 
Create a circle level set with binary values. 
skimage.segmentation.checkerboard_level_set (…) 
Create a checkerboard level set with binary values. 
skimage.segmentation.flood (image, seed_point, *) 
Mask corresponding to a flood fill. 
skimage.segmentation.flood_fill (image, …) 
Perform flood filling on an image. 
skimage.segmentation.
random_walker
(data, labels, beta=130, mode='bf', tol=0.001, copy=True, multichannel=False, return_full_prob=False, spacing=None)[source]¶Random walker algorithm for segmentation from markers.
Random walker algorithm is implemented for graylevel or multichannel images.
Parameters: 


Returns: 

See also
skimage.morphology.watershed
Notes
Multichannel inputs are scaled with all channel data combined. Ensure all channels are separately normalized prior to running this algorithm.
The spacing argument is specifically for anisotropic datasets, where data points are spaced differently in one or more spatial dimensions. Anisotropic data is commonly encountered in medical imaging.
The algorithm was first proposed in [1].
The algorithm solves the diffusion equation at infinite times for sources placed on markers of each phase in turn. A pixel is labeled with the phase that has the greatest probability to diffuse first to the pixel.
The diffusion equation is solved by minimizing x.T L x for each phase, where L is the Laplacian of the weighted graph of the image, and x is the probability that a marker of the given phase arrives first at a pixel by diffusion (x=1 on markers of the phase, x=0 on the other markers, and the other coefficients are looked for). Each pixel is attributed the label for which it has a maximal value of x. The Laplacian L of the image is defined as:
 L_ii = d_i, the number of neighbors of pixel i (the degree of i)
 L_ij = w_ij if i and j are adjacent pixels
The weight w_ij is a decreasing function of the norm of the local gradient. This ensures that diffusion is easier between pixels of similar values.
When the Laplacian is decomposed into blocks of marked and unmarked pixels:
L = M B.T
B A
with first indices corresponding to marked pixels, and then to unmarked pixels, minimizing x.T L x for one phase amount to solving:
A x =  B x_m
where x_m = 1 on markers of the given phase, and 0 on other markers. This linear system is solved in the algorithm using a direct method for small images, and an iterative method for larger images.
References
[1]  (1, 2) Leo Grady, Random walks for image segmentation, IEEE Trans Pattern Anal Mach Intell. 2006 Nov;28(11):176883. DOI:10.1109/TPAMI.2006.233. 
Examples
>>> np.random.seed(0)
>>> a = np.zeros((10, 10)) + 0.2 * np.random.rand(10, 10)
>>> a[5:8, 5:8] += 1
>>> b = np.zeros_like(a)
>>> b[3, 3] = 1 # Marker for first phase
>>> b[6, 6] = 2 # Marker for second phase
>>> random_walker(a, b)
array([[1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 2, 2, 2, 1, 1],
[1, 1, 1, 1, 1, 2, 2, 2, 1, 1],
[1, 1, 1, 1, 1, 2, 2, 2, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1]], dtype=int32)
skimage.segmentation.random_walker
¶skimage.segmentation.
active_contour
(image, snake, alpha=0.01, beta=0.1, w_line=0, w_edge=1, gamma=0.01, bc='periodic', max_px_move=1.0, max_iterations=2500, convergence=0.1)[source]¶Active contour model.
Active contours by fitting snakes to features of images. Supports single and multichannel 2D images. Snakes can be periodic (for segmentation) or have fixed and/or free ends. The output snake has the same length as the input boundary. As the number of points is constant, make sure that the initial snake has enough points to capture the details of the final contour.
Parameters: 


Returns: 

References
[1]  Kass, M.; Witkin, A.; Terzopoulos, D. “Snakes: Active contour models”. International Journal of Computer Vision 1 (4): 321 (1988). DOI:10.1007/BF00133570 
Examples
>>> from skimage.draw import circle_perimeter
>>> from skimage.filters import gaussian
Create and smooth image:
>>> img = np.zeros((100, 100))
>>> rr, cc = circle_perimeter(35, 45, 25)
>>> img[rr, cc] = 1
>>> img = gaussian(img, 2)
Initialize spline:
>>> s = np.linspace(0, 2*np.pi, 100)
>>> init = 50 * np.array([np.cos(s), np.sin(s)]).T + 50
Fit spline to image:
>>> snake = active_contour(img, init, w_edge=0, w_line=1) #doctest: +SKIP
>>> dist = np.sqrt((45snake[:, 0])**2 + (35snake[:, 1])**2) #doctest: +SKIP
>>> int(np.mean(dist)) #doctest: +SKIP
25
skimage.segmentation.active_contour
¶skimage.segmentation.
felzenszwalb
(image, scale=1, sigma=0.8, min_size=20, multichannel=True)[source]¶Computes Felsenszwalb’s efficient graph based image segmentation.
Produces an oversegmentation of a multichannel (i.e. RGB) image
using a fast, minimum spanning tree based clustering on the image grid.
The parameter scale
sets an observation level. Higher scale means
less and larger segments. sigma
is the diameter of a Gaussian kernel,
used for smoothing the image prior to segmentation.
The number of produced segments as well as their size can only be
controlled indirectly through scale
. Segment size within an image can
vary greatly depending on local contrast.
For RGB images, the algorithm uses the euclidean distance between pixels in color space.
Parameters: 


Returns: 

Notes
The k parameter used in the original paper renamed to scale here.
References
[1]  Efficient graphbased image segmentation, Felzenszwalb, P.F. and Huttenlocher, D.P. International Journal of Computer Vision, 2004 
Examples
>>> from skimage.segmentation import felzenszwalb
>>> from skimage.data import coffee
>>> img = coffee()
>>> segments = felzenszwalb(img, scale=3.0, sigma=0.95, min_size=5)
skimage.segmentation.felzenszwalb
¶skimage.segmentation.
slic
(image, n_segments=100, compactness=10.0, max_iter=10, sigma=0, spacing=None, multichannel=True, convert2lab=None, enforce_connectivity=True, min_size_factor=0.5, max_size_factor=3, slic_zero=False)[source]¶Segments image using kmeans clustering in Color(x,y,z) space.
Parameters: 


Returns: 

Raises: 

Notes
sigma=1
and spacing=[5, 1, 1]
, the effective sigma is [0.2, 1, 1]
. This
ensures sensible smoothing for anisotropic images.References
[1]  Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Süsstrunk, SLIC Superpixels Compared to Stateoftheart Superpixel Methods, TPAMI, May 2012. 
[2]  (1, 2) http://ivrg.epfl.ch/research/superpixels#SLICO 
Examples
>>> from skimage.segmentation import slic
>>> from skimage.data import astronaut
>>> img = astronaut()
>>> segments = slic(img, n_segments=100, compactness=10)
Increasing the compactness parameter yields more square regions:
>>> segments = slic(img, n_segments=100, compactness=20)
skimage.segmentation.
quickshift
(image, ratio=1.0, kernel_size=5, max_dist=10, return_tree=False, sigma=0, convert2lab=True, random_seed=42)[source]¶Segments image using quickshift clustering in Color(x,y) space.
Produces an oversegmentation of the image using the quickshift modeseeking algorithm.
Parameters: 


Returns: 

Notes
The authors advocate to convert the image to Lab color space prior to segmentation, though this is not strictly necessary. For this to work, the image must be given in RGB format.
References
[1]  Quick shift and kernel methods for mode seeking, Vedaldi, A. and Soatto, S. European Conference on Computer Vision, 2008 
skimage.segmentation.quickshift
¶skimage.segmentation.
find_boundaries
(label_img, connectivity=1, mode='thick', background=0)[source]¶Return bool array where boundaries between labeled regions are True.
Parameters: 


Returns: 

Examples
>>> labels = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
... [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
... [0, 0, 0, 0, 0, 5, 5, 5, 0, 0],
... [0, 0, 1, 1, 1, 5, 5, 5, 0, 0],
... [0, 0, 1, 1, 1, 5, 5, 5, 0, 0],
... [0, 0, 1, 1, 1, 5, 5, 5, 0, 0],
... [0, 0, 0, 0, 0, 5, 5, 5, 0, 0],
... [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
... [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=np.uint8)
>>> find_boundaries(labels, mode='thick').astype(np.uint8)
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 1, 1, 1, 1, 1, 0, 1, 1, 0],
[0, 1, 1, 0, 1, 1, 0, 1, 1, 0],
[0, 1, 1, 1, 1, 1, 0, 1, 1, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
>>> find_boundaries(labels, mode='inner').astype(np.uint8)
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 0, 1, 0, 0],
[0, 0, 1, 0, 1, 1, 0, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 0, 1, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
>>> find_boundaries(labels, mode='outer').astype(np.uint8)
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 0, 0, 1, 0],
[0, 1, 0, 0, 1, 1, 0, 0, 1, 0],
[0, 1, 0, 0, 1, 1, 0, 0, 1, 0],
[0, 1, 0, 0, 1, 1, 0, 0, 1, 0],
[0, 0, 1, 1, 1, 1, 0, 0, 1, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
>>> labels_small = labels[::2, ::3]
>>> labels_small
array([[0, 0, 0, 0],
[0, 0, 5, 0],
[0, 1, 5, 0],
[0, 0, 5, 0],
[0, 0, 0, 0]], dtype=uint8)
>>> find_boundaries(labels_small, mode='subpixel').astype(np.uint8)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 0],
[0, 0, 0, 1, 0, 1, 0],
[0, 1, 1, 1, 0, 1, 0],
[0, 1, 0, 1, 0, 1, 0],
[0, 1, 1, 1, 0, 1, 0],
[0, 0, 0, 1, 0, 1, 0],
[0, 0, 0, 1, 1, 1, 0],
[0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
>>> bool_image = np.array([[False, False, False, False, False],
... [False, False, False, False, False],
... [False, False, True, True, True],
... [False, False, True, True, True],
... [False, False, True, True, True]], dtype=np.bool)
>>> find_boundaries(bool_image)
array([[False, False, False, False, False],
[False, False, True, True, True],
[False, True, True, True, True],
[False, True, True, False, False],
[False, True, True, False, False]], dtype=bool)
skimage.segmentation.
mark_boundaries
(image, label_img, color=(1, 1, 0), outline_color=None, mode='outer', background_label=0)[source]¶Return image with boundaries between labeled regions highlighted.
Parameters: 


Returns: 

See also
skimage.segmentation.
clear_border
(labels, buffer_size=0, bgval=0, in_place=False, mask=None)[source]¶Clear objects connected to the label image border.
Parameters: 


Examples
>>> import numpy as np
>>> from skimage.segmentation import clear_border
>>> labels = np.array([[0, 0, 0, 0, 0, 0, 0, 1, 0],
... [1, 1, 0, 0, 1, 0, 0, 1, 0],
... [1, 1, 0, 1, 0, 1, 0, 0, 0],
... [0, 0, 0, 1, 1, 1, 1, 0, 0],
... [0, 1, 1, 1, 1, 1, 1, 1, 0],
... [0, 0, 0, 0, 0, 0, 0, 0, 0]])
>>> clear_border(labels)
array([[0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0]])
>>> mask = np.array([[0, 0, 1, 1, 1, 1, 1, 1, 1],
... [0, 0, 1, 1, 1, 1, 1, 1, 1],
... [1, 1, 1, 1, 1, 1, 1, 1, 1],
... [1, 1, 1, 1, 1, 1, 1, 1, 1],
... [1, 1, 1, 1, 1, 1, 1, 1, 1],
... [1, 1, 1, 1, 1, 1, 1, 1, 1]]).astype(np.bool)
>>> clear_border(labels, mask=mask)
array([[0, 0, 0, 0, 0, 0, 0, 1, 0],
[0, 0, 0, 0, 1, 0, 0, 1, 0],
[0, 0, 0, 1, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0]])
skimage.segmentation.clear_border
¶skimage.segmentation.
join_segmentations
(s1, s2)[source]¶Return the join of the two input segmentations.
The join J of S1 and S2 is defined as the segmentation in which two voxels are in the same segment if and only if they are in the same segment in both S1 and S2.
Parameters: 


Returns: 

Examples
>>> from skimage.segmentation import join_segmentations
>>> s1 = np.array([[0, 0, 1, 1],
... [0, 2, 1, 1],
... [2, 2, 2, 1]])
>>> s2 = np.array([[0, 1, 1, 0],
... [0, 1, 1, 0],
... [0, 1, 1, 1]])
>>> join_segmentations(s1, s2)
array([[0, 1, 3, 2],
[0, 5, 3, 2],
[4, 5, 5, 3]])
skimage.segmentation.join_segmentations
¶skimage.segmentation.
relabel_sequential
(label_field, offset=1)[source]¶Relabel arbitrary labels to {offset, … offset + number_of_labels}.
This function also returns the forward map (mapping the original labels to the reduced labels) and the inverse map (mapping the reduced labels back to the original ones).
Parameters: 


Returns: 

Notes
The label 0 is assumed to denote the background and is never remapped.
The forward map can be extremely big for some inputs, since its
length is given by the maximum of the label field. However, in most
situations, label_field.max()
is much smaller than
label_field.size
, and in these cases the forward map is
guaranteed to be smaller than either the input or output images.
Examples
>>> from skimage.segmentation import relabel_sequential
>>> label_field = np.array([1, 1, 5, 5, 8, 99, 42])
>>> relab, fw, inv = relabel_sequential(label_field)
>>> relab
array([1, 1, 2, 2, 3, 5, 4])
>>> fw
array([0, 1, 0, 0, 0, 2, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 5])
>>> inv
array([ 0, 1, 5, 8, 42, 99])
>>> (fw[label_field] == relab).all()
True
>>> (inv[relab] == label_field).all()
True
>>> relab, fw, inv = relabel_sequential(label_field, offset=5)
>>> relab
array([5, 5, 6, 6, 7, 9, 8])
skimage.segmentation.
watershed
(image, markers, connectivity=1, offset=None, mask=None, compactness=0, watershed_line=False)[source]¶Find watershed basins in image flooded from given markers.
Parameters: 


Returns: 

See also
skimage.segmentation.random_walker
Notes
This function implements a watershed algorithm [1] [2] that apportions pixels into marked basins. The algorithm uses a priority queue to hold the pixels with the metric for the priority queue being pixel value, then the time of entry into the queue  this settles ties in favor of the closest marker.
Some ideas taken from Soille, “Automated Basin Delineation from Digital Elevation Models Using Mathematical Morphology”, Signal Processing 20 (1990) 171182
The most important insight in the paper is that entry time onto the queue solves two problems: a pixel should be assigned to the neighbor with the largest gradient or, if there is no gradient, pixels on a plateau should be split between markers on opposite sides.
This implementation converts all arguments to specific, lowest common denominator types, then passes these to a C algorithm.
Markers can be determined manually, or automatically using for example the local minima of the gradient of the image, or the local maxima of the distance function to the background for separating overlapping objects (see example).
References
[1]  (1, 2) https://en.wikipedia.org/wiki/Watershed_%28image_processing%29 
[2]  (1, 2) http://cmm.ensmp.fr/~beucher/wtshed.html 
[3]  (1, 2) Peer Neubert & Peter Protzel (2014). Compact Watershed and Preemptive SLIC: On Improving Tradeoffs of Superpixel Segmentation Algorithms. ICPR 2014, pp 9961001. DOI:10.1109/ICPR.2014.181 https://www.tuchemnitz.de/etit/proaut/forschung/rsrc/cws_pSLIC_ICPR.pdf 
Examples
The watershed algorithm is useful to separate overlapping objects.
We first generate an initial image with two overlapping circles:
>>> x, y = np.indices((80, 80))
>>> x1, y1, x2, y2 = 28, 28, 44, 52
>>> r1, r2 = 16, 20
>>> mask_circle1 = (x  x1)**2 + (y  y1)**2 < r1**2
>>> mask_circle2 = (x  x2)**2 + (y  y2)**2 < r2**2
>>> image = np.logical_or(mask_circle1, mask_circle2)
Next, we want to separate the two circles. We generate markers at the maxima of the distance to the background:
>>> from scipy import ndimage as ndi
>>> distance = ndi.distance_transform_edt(image)
>>> from skimage.feature import peak_local_max
>>> local_maxi = peak_local_max(distance, labels=image,
... footprint=np.ones((3, 3)),
... indices=False)
>>> markers = ndi.label(local_maxi)[0]
Finally, we run the watershed on the image and markers:
>>> labels = watershed(distance, markers, mask=image)
The algorithm works also for 3D images, and can be used for example to separate overlapping spheres.
skimage.segmentation.watershed
¶skimage.segmentation.
chan_vese
(image, mu=0.25, lambda1=1.0, lambda2=1.0, tol=0.001, max_iter=500, dt=0.5, init_level_set='checkerboard', extended_output=False)[source]¶ChanVese segmentation algorithm.
Active contour model by evolving a level set. Can be used to segment objects without clearly defined boundaries.
Parameters: 


Returns: 

Notes
The ChanVese Algorithm is designed to segment objects without clearly defined boundaries. This algorithm is based on level sets that are evolved iteratively to minimize an energy, which is defined by weighted values corresponding to the sum of differences intensity from the average value outside the segmented region, the sum of differences from the average value inside the segmented region, and a term which is dependent on the length of the boundary of the segmented region.
This algorithm was first proposed by Tony Chan and Luminita Vese, in a publication entitled “An Active Contour Model Without Edges” [1].
This implementation of the algorithm is somewhat simplified in the sense that the area factor ‘nu’ described in the original paper is not implemented, and is only suitable for grayscale images.
Typical values for lambda1 and lambda2 are 1. If the ‘background’ is very different from the segmented object in terms of distribution (for example, a uniform black image with figures of varying intensity), then these values should be different from each other.
Typical values for mu are between 0 and 1, though higher values can be used when dealing with shapes with very illdefined contours.
The ‘energy’ which this algorithm tries to minimize is defined as the sum of the differences from the average within the region squared and weighed by the ‘lambda’ factors to which is added the length of the contour multiplied by the ‘mu’ factor.
Supports 2D grayscale images only, and does not implement the area term described in the original article.
References
[1]  (1, 2) An Active Contour Model without Edges, Tony Chan and Luminita Vese, ScaleSpace Theories in Computer Vision, 1999, DOI:10.1007/3540482369_13 
[2]  ChanVese Segmentation, Pascal Getreuer Image Processing On Line, 2 (2012), pp. 214224, DOI:10.5201/ipol.2012.gcv 
[3]  The ChanVese Algorithm  Project Report, Rami Cohen, 2011 arXiv:1107.2782 
skimage.segmentation.chan_vese
¶skimage.segmentation.
morphological_geodesic_active_contour
(gimage, iterations, init_level_set='circle', smoothing=1, threshold='auto', balloon=0, iter_callback=<function <lambda>>)[source]¶Morphological Geodesic Active Contours (MorphGAC).
Geodesic active contours implemented with morphological operators. It can be used to segment objects with visible but noisy, cluttered, broken borders.
Parameters: 


Returns: 

Notes
This is a version of the Geodesic Active Contours (GAC) algorithm that uses morphological operators instead of solving partial differential equations (PDEs) for the evolution of the contour. The set of morphological operators used in this algorithm are proved to be infinitesimally equivalent to the GAC PDEs (see [1]). However, morphological operators are do not suffer from the numerical stability issues typically found in PDEs (e.g., it is not necessary to find the right time step for the evolution), and are computationally faster.
The algorithm and its theoretical derivation are described in [1].
References
[1]  (1, 2, 3) A Morphological Approach to Curvaturebased Evolution of Curves and Surfaces, Pablo MárquezNeila, Luis Baumela, Luis Álvarez. In IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 2014, DOI:10.1109/TPAMI.2013.106 
skimage.segmentation.morphological_geodesic_active_contour
¶skimage.segmentation.
morphological_chan_vese
(image, iterations, init_level_set='checkerboard', smoothing=1, lambda1=1, lambda2=1, iter_callback=<function <lambda>>)[source]¶Morphological Active Contours without Edges (MorphACWE)
Active contours without edges implemented with morphological operators. It can be used to segment objects in images and volumes without well defined borders. It is required that the inside of the object looks different on average than the outside (i.e., the inner area of the object should be darker or lighter than the outer area on average).
Parameters: 


Returns: 

See also
Notes
This is a version of the ChanVese algorithm that uses morphological operators instead of solving a partial differential equation (PDE) for the evolution of the contour. The set of morphological operators used in this algorithm are proved to be infinitesimally equivalent to the ChanVese PDE (see [1]). However, morphological operators are do not suffer from the numerical stability issues typically found in PDEs (it is not necessary to find the right time step for the evolution), and are computationally faster.
The algorithm and its theoretical derivation are described in [1].
References
[1]  (1, 2, 3) A Morphological Approach to Curvaturebased Evolution of Curves and Surfaces, Pablo MárquezNeila, Luis Baumela, Luis Álvarez. In IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 2014, DOI:10.1109/TPAMI.2013.106 
skimage.segmentation.morphological_chan_vese
¶skimage.segmentation.
inverse_gaussian_gradient
(image, alpha=100.0, sigma=5.0)[source]¶Inverse of gradient magnitude.
Compute the magnitude of the gradients in the image and then inverts the result in the range [0, 1]. Flat areas are assigned values close to 1, while areas close to borders are assigned values close to 0.
This function or a similar one defined by the user should be applied over the image as a preprocessing step before calling morphological_geodesic_active_contour.
Parameters: 


Returns: 

skimage.segmentation.inverse_gaussian_gradient
¶skimage.segmentation.
circle_level_set
(image_shape, center=None, radius=None)[source]¶Create a circle level set with binary values.
Parameters: 


Returns: 

See also
skimage.segmentation.
checkerboard_level_set
(image_shape, square_size=5)[source]¶Create a checkerboard level set with binary values.
Parameters: 


Returns: 

See also
skimage.segmentation.checkerboard_level_set
¶skimage.segmentation.
flood
(image, seed_point, *, selem=None, connectivity=None, tolerance=None)[source]¶Mask corresponding to a flood fill.
Starting at a specific seed_point, connected points equal or within tolerance of the seed value are found.
Parameters: 


Returns: 

Notes
The conceptual analogy of this operation is the ‘paint bucket’ tool in many raster graphics programs. This function returns just the mask representing the fill.
If indices are desired rather than masks for memory reasons, the user can simply run numpy.nonzero on the result, save the indices, and discard this mask.
Examples
>>> from skimage.morphology import flood
>>> image = np.zeros((4, 7), dtype=int)
>>> image[1:3, 1:3] = 1
>>> image[3, 0] = 1
>>> image[1:3, 4:6] = 2
>>> image[3, 6] = 3
>>> image
array([[0, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 0, 2, 2, 0],
[0, 1, 1, 0, 2, 2, 0],
[1, 0, 0, 0, 0, 0, 3]])
Fill connected ones with 5, with full connectivity (diagonals included):
>>> mask = flood(image, (1, 1))
>>> image_flooded = image.copy()
>>> image_flooded[mask] = 5
>>> image_flooded
array([[0, 0, 0, 0, 0, 0, 0],
[0, 5, 5, 0, 2, 2, 0],
[0, 5, 5, 0, 2, 2, 0],
[5, 0, 0, 0, 0, 0, 3]])
Fill connected ones with 5, excluding diagonal points (connectivity 1):
>>> mask = flood(image, (1, 1), connectivity=1)
>>> image_flooded = image.copy()
>>> image_flooded[mask] = 5
>>> image_flooded
array([[0, 0, 0, 0, 0, 0, 0],
[0, 5, 5, 0, 2, 2, 0],
[0, 5, 5, 0, 2, 2, 0],
[1, 0, 0, 0, 0, 0, 3]])
Fill with a tolerance:
>>> mask = flood(image, (0, 0), tolerance=1)
>>> image_flooded = image.copy()
>>> image_flooded[mask] = 5
>>> image_flooded
array([[5, 5, 5, 5, 5, 5, 5],
[5, 5, 5, 5, 2, 2, 5],
[5, 5, 5, 5, 2, 2, 5],
[5, 5, 5, 5, 5, 5, 3]])
skimage.segmentation.flood
¶skimage.segmentation.
flood_fill
(image, seed_point, new_value, *, selem=None, connectivity=None, tolerance=None, inplace=False)[source]¶Perform flood filling on an image.
Starting at a specific seed_point, connected points equal or within tolerance of the seed value are found, then set to new_value.
Parameters: 


Returns: 

Notes
The conceptual analogy of this operation is the ‘paint bucket’ tool in many raster graphics programs.
Examples
>>> from skimage.morphology import flood_fill
>>> image = np.zeros((4, 7), dtype=int)
>>> image[1:3, 1:3] = 1
>>> image[3, 0] = 1
>>> image[1:3, 4:6] = 2
>>> image[3, 6] = 3
>>> image
array([[0, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 0, 2, 2, 0],
[0, 1, 1, 0, 2, 2, 0],
[1, 0, 0, 0, 0, 0, 3]])
Fill connected ones with 5, with full connectivity (diagonals included):
>>> flood_fill(image, (1, 1), 5)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 5, 5, 0, 2, 2, 0],
[0, 5, 5, 0, 2, 2, 0],
[5, 0, 0, 0, 0, 0, 3]])
Fill connected ones with 5, excluding diagonal points (connectivity 1):
>>> flood_fill(image, (1, 1), 5, connectivity=1)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 5, 5, 0, 2, 2, 0],
[0, 5, 5, 0, 2, 2, 0],
[1, 0, 0, 0, 0, 0, 3]])
Fill with a tolerance:
>>> flood_fill(image, (0, 0), 5, tolerance=1)
array([[5, 5, 5, 5, 5, 5, 5],
[5, 5, 5, 5, 2, 2, 5],
[5, 5, 5, 5, 2, 2, 5],
[5, 5, 5, 5, 5, 5, 3]])
skimage.segmentation.flood_fill
¶