# 3.3. `scikit-image`: image processing¶

Author: Emmanuelle Gouillart

scikit-image is a Python package dedicated to image processing, using NumPy arrays as image objects. This chapter describes how to use `scikit-image` for various image processing tasks, and how it relates to other scientific Python modules such as NumPy and SciPy.

For basic image manipulation, such as image cropping or simple filtering, a large number of simple operations can be realized with NumPy and SciPy only. See Image manipulation and processing using NumPy and SciPy.

Note that you should be familiar with the content of the previous chapter before reading the current one, as basic operations such as masking and labeling are a prerequisite.

## 3.3.1. Introduction and concepts¶

Images are NumPy’s arrays `np.ndarray`

image:

`np.ndarray`

pixels:

array values: `a[2, 3]`

channels:

array dimensions

image encoding:

`dtype` (`np.uint8`, `np.uint16`, `np.float`)

filters:

functions (`numpy`, `skimage`, `scipy`)

```>>> import numpy as np
>>> check = np.zeros((8, 8))
>>> check[::2, 1::2] = 1
>>> check[1::2, ::2] = 1
>>> import matplotlib.pyplot as plt
>>> plt.imshow(check, cmap='gray', interpolation='nearest')
<matplotlib.image.AxesImage object at ...>
``` ### 3.3.1.1. `scikit-image` and the scientific Python ecosystem¶

`scikit-image` is packaged in both `pip` and `conda`-based Python installations, as well as in most Linux distributions. Other Python packages for image processing & visualization that operate on NumPy arrays include:

`scipy.ndimage`

For N-dimensional arrays. Basic filtering, mathematical morphology, regions properties

Mahotas

With a focus on high-speed implementations.

Napari

A fast, interactive, multi-dimensional image viewer built in Qt.

Some powerful C++ image processing libraries also have Python bindings:

OpenCV

A highly optimized computer vision library with a focus on real-time applications.

ITK

The Insight ToolKit, especially useful for registration and working with 3D images.

To varying degrees, these tend to be less Pythonic and NumPy-friendly.

### 3.3.1.2. What is included in scikit-image¶

The library contains predominantly image processing algorithms, but also utility functions to ease data handling and processing. It contains the following submodules:

`color`

Color space conversion.

`data`

Test images and example data.

`draw`

Drawing primitives (lines, text, etc.) that operate on NumPy arrays.

`exposure`

Image intensity adjustment, e.g., histogram equalization, etc.

`feature`

Feature detection and extraction, e.g., texture analysis corners, etc.

`filters`

Sharpening, edge finding, rank filters, thresholding, etc.

`graph`

Graph-theoretic operations, e.g., shortest paths.

`io`

Reading, saving, and displaying images and video.

`measure`

Measurement of image properties, e.g., region properties and contours.

`metrics`

Metrics corresponding to images, e.g. distance metrics, similarity, etc.

`morphology`

Morphological operations, e.g., opening or skeletonization.

`restoration`

Restoration algorithms, e.g., deconvolution algorithms, denoising, etc.

`segmentation`

Partitioning an image into multiple regions.

`transform`

Geometric and other transforms, e.g., rotation or the Radon transform.

`util`

Generic utilities.

## 3.3.2. Importing¶

We import `scikit-image` using the convention:

```>>> import skimage as ski
```

Most functionality lives in subpackages, e.g.:

```>>> image = ski.data.cat()
```

You can list all submodules with:

```>>> for m in dir(ski): print(m)
__version__
color
data
draw
exposure
feature
filters
future
graph
io
measure
metrics
morphology
registration
restoration
segmentation
transform
util
```

Most `scikit-image` functions take NumPy `ndarrays` as arguments

```>>> camera = ski.data.camera()
>>> camera.dtype
dtype('uint8')
>>> camera.shape
(512, 512)
>>> filtered_camera = ski.filters.gaussian(camera, sigma=1)
>>> type(filtered_camera)
<class 'numpy.ndarray'>
```

## 3.3.3. Example data¶

To start off, we need example images to work with. The library ships with a few of these:

`skimage.data`

```>>> image = ski.data.cat()
>>> image.shape
(300, 451, 3)
```

## 3.3.4. Input/output, data types and colorspaces¶

Save an image to disk: `skimage.io.imsave()`

```>>> ski.io.imsave("cat.png", image)
```

Reading from files: `skimage.io.imread()`

```>>> cat = ski.io.imread("cat.png")
``` This works with many data formats supported by the ImageIO library.

```>>> logo = ski.io.imread('https://scikit-image.org/_static/img/logo.png')
```

### 3.3.4.1. Data types¶ Image ndarrays can be represented either by integers (signed or unsigned) or floats.

Careful with overflows with integer data types

```>>> camera = ski.data.camera()
>>> camera.dtype
dtype('uint8')
>>> camera_multiply = 3 * camera
```

Different integer sizes are possible: 8-, 16- or 32-bytes, signed or unsigned.

Warning

An important (if questionable) `skimage` convention: float images are supposed to lie in [-1, 1] (in order to have comparable contrast for all float images)

```>>> camera_float = ski.util.img_as_float(camera)
>>> camera.max(), camera_float.max()
(255, 1.0)
```

Some image processing routines need to work with float arrays, and may hence output an array with a different type and the data range from the input array

```>>> camera_sobel = ski.filters.sobel(camera)
>>> camera_sobel.max()
0.644...
```

Utility functions are provided in `skimage` to convert both the dtype and the data range, following skimage’s conventions: `util.img_as_float`, `util.img_as_ubyte`, etc.

See the user guide for more details.

### 3.3.4.2. Colorspaces¶

Color images are of shape (N, M, 3) or (N, M, 4) (when an alpha channel encodes transparency)

```>>> face = sp.datasets.face()
>>> face.shape
(768, 1024, 3)
```

Routines converting between different colorspaces (RGB, HSV, LAB etc.) are available in `skimage.color` : `color.rgb2hsv`, `color.lab2rgb`, etc. Check the docstring for the expected dtype (and data range) of input images.

## 3.3.5. Image preprocessing / enhancement¶

Goals: denoising, feature (edges) extraction, …

### 3.3.5.1. Local filters¶

Local filters replace the value of pixels by a function of the values of neighboring pixels. The function can be linear or non-linear.

Neighbourhood: square (choose size), disk, or more complicated structuring element. Example : horizontal Sobel filter

```>>> text = ski.data.text()
>>> hsobel_text = ski.filters.sobel_h(text)
```

Uses the following linear kernel for computing horizontal gradients:

```1   2   1
0   0   0
-1  -2  -1
``` ### 3.3.5.2. Non-local filters¶

Non-local filters use a large region of the image (or all the image) to transform the value of one pixel:

```>>> camera = ski.data.camera()
>>> camera_equalized = ski.exposure.equalize_hist(camera)
```

Enhances contrast in large almost uniform regions. ### 3.3.5.3. Mathematical morphology¶

See wikipedia for an introduction on mathematical morphology.

Probe an image with a simple shape (a structuring element), and modify this image according to how the shape locally fits or misses the image.

Default structuring element: 4-connectivity of a pixel

```>>> # Import structuring elements to make them more easily accessible
>>> from skimage.morphology import disk, diamond

>>> diamond(1)
array([[0, 1, 0],
[1, 1, 1],
[0, 1, 0]], dtype=uint8)
``` Erosion = minimum filter. Replace the value of a pixel by the minimal value covered by the structuring element.:

```>>> a = np.zeros((7,7), dtype=np.uint8)
>>> a[1:6, 2:5] = 1
>>> a
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
>>> ski.morphology.binary_erosion(a, diamond(1)).astype(np.uint8)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
>>> #Erosion removes objects smaller than the structure
>>> ski.morphology.binary_erosion(a, diamond(2)).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, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
```

Dilation: maximum filter:

```>>> a = np.zeros((5, 5))
>>> a[2, 2] = 1
>>> a
array([[0.,  0.,  0.,  0.,  0.],
[0.,  0.,  0.,  0.,  0.],
[0.,  0.,  1.,  0.,  0.],
[0.,  0.,  0.,  0.,  0.],
[0.,  0.,  0.,  0.,  0.]])
>>> ski.morphology.binary_dilation(a, diamond(1)).astype(np.uint8)
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0]], dtype=uint8)
```

Opening: erosion + dilation:

```>>> a = np.zeros((5,5), dtype=int)
>>> a[1:4, 1:4] = 1; a[4, 4] = 1
>>> a
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 1]])
>>> ski.morphology.binary_opening(a, diamond(1)).astype(np.uint8)
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0]], dtype=uint8)
```

Opening removes small objects and smoothes corners.

Higher-level mathematical morphology are available: tophat, skeletonization, etc.

Basic mathematical morphology is also implemented in `scipy.ndimage.morphology`. The `scipy.ndimage` implementation works on arbitrary-dimensional arrays.

## 3.3.6. Image segmentation¶

Image segmentation is the attribution of different labels to different regions of the image, for example in order to extract the pixels of an object of interest.

### 3.3.6.1. Binary segmentation: foreground + background¶

#### Histogram-based method: Otsu thresholding¶

Tip

The Otsu method is a simple heuristic to find a threshold to separate the foreground from the background.

```camera = ski.data.camera()
val = ski.filters.threshold_otsu(camera)
``` #### Labeling connected components of a discrete image¶

Tip

Once you have separated foreground objects, it is use to separate them from each other. For this, we can assign a different integer labels to each one.

Synthetic data:

```>>> n = 20
>>> l = 256
>>> im = np.zeros((l, l))
>>> rng = np.random.default_rng()
>>> points = l * rng.random((2, n ** 2))
>>> im[(points).astype(int), (points).astype(int)] = 1
>>> im = ski.filters.gaussian(im, sigma=l / (4. * n))
>>> blobs = im > im.mean()
```

Label all connected components:

```>>> all_labels = ski.measure.label(blobs)
```

Label only foreground connected components:

```>>> blobs_labels = ski.measure.label(blobs, background=0)
``` `scipy.ndimage.find_objects()` is useful to return slices on object in an image.

### 3.3.6.2. Marker based methods¶

If you have markers inside a set of regions, you can use these to segment the regions.

#### Watershed segmentation¶

The Watershed (`skimage.segmentation.watershed()`) is a region-growing approach that fills “basins” in the image

```>>> # 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
>>> # Now we want to separate the two objects in image
>>> # Generate the markers as local maxima of the distance
>>> # to the background
>>> import scipy as sp
>>> distance = sp.ndimage.distance_transform_edt(image)
>>> peak_idx = ski.feature.peak_local_max(
...     distance, footprint=np.ones((3, 3)), labels=image
... )
>>> labels_ws = ski.segmentation.watershed(
... )
```

#### Random walker segmentation¶

The random walker algorithm (`skimage.segmentation.random_walker()`) is similar to the Watershed, but with a more “probabilistic” approach. It is based on the idea of the diffusion of labels in the image:

```>>> # Transform markers image so that 0-valued pixels are to
>>> # be labelled, and -1-valued pixels represent background
>>> markers[~image] = -1
>>> labels_rw = ski.segmentation.random_walker(image, markers)
``` ## 3.3.7. Measuring regions’ properties¶

Example: compute the size and perimeter of the two segmented regions:

```>>> properties = ski.measure.regionprops(labels_rw)
>>> [float(prop.area) for prop in properties]
[770.0, 1168.0]
>>> [prop.perimeter for prop in properties]
[100.91..., 126.81...]
```

for some properties, functions are available as well in `scipy.ndimage.measurements` with a different API (a list is returned).

## 3.3.8. Data visualization and interaction¶

Meaningful visualizations are useful when testing a given processing pipeline.

Some image processing operations:

```>>> coins = ski.data.coins()
>>> mask = coins > ski.filters.threshold_otsu(coins)
```

Visualize binary result:

```>>> plt.figure()
<Figure size ... with 0 Axes>
>>> plt.imshow(clean_border, cmap='gray')
<matplotlib.image.AxesImage object at 0x...>
```

Visualize contour

```>>> plt.figure()
<Figure size ... with 0 Axes>
>>> plt.imshow(coins, cmap='gray')
<matplotlib.image.AxesImage object at 0x...>
>>> plt.contour(clean_border, [0.5])
```

Use `skimage` dedicated utility function:

```>>> coins_edges = ski.segmentation.mark_boundaries(
...     coins, clean_border.astype(int)
... )
``` ## 3.3.9. Feature extraction for computer vision¶

Geometric or textural descriptor can be extracted from images in order to

• classify parts of the image (e.g. sky vs. buildings)

• match parts of different images (e.g. for object detection)

• and many other applications of Computer Vision

Example: detecting corners using Harris detector

```tform = ski.transform.AffineTransform(
scale=(1.3, 1.1), rotation=1, shear=0.7,
translation=(210, 50)
)
image = ski.transform.warp(
data.checkerboard(), tform.inverse, output_shape=(350, 350)
)

coords = ski.feature.corner_peaks(
ski.feature.corner_harris(image), min_distance=5
)
coords_subpix = ski.feature.corner_subpix(
image, coords, window_size=13
)
``` (this example is taken from the plot_corner example in scikit-image)

Points of interest such as corners can then be used to match objects in different images, as described in the plot_matching example of scikit-image.

## 3.3.11. Examples for the scikit-image chapter¶ Creating an image

Creating an image Displaying a simple image

Displaying a simple image Integers can overflow

Integers can overflow Equalizing the histogram of an image

Equalizing the histogram of an image Computing horizontal gradients with the Sobel filter

Computing horizontal gradients with the Sobel filter Segmentation contours

Segmentation contours Otsu thresholding

Otsu thresholding Affine transform

Affine transform Labelling connected components of an image

Labelling connected components of an image Various denoising filters

Various denoising filters Watershed and random walker for segmentation

Watershed and random walker for segmentation

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