Filter overview

Filter overview#

In this notebook we demonstrate some more typical filters using the nuclei example image.

import numpy as np

import matplotlib.pyplot as plt
from skimage.io import imread
from skimage import data
from skimage import filters
from skimage import morphology
from scipy.ndimage import convolve, gaussian_laplace
import stackview

image3 = imread('../../data/mitosis_mod.tif').astype(float)

plt.imshow(image3, cmap='gray')

<matplotlib.image.AxesImage at 0x12d1b7ce940>
../_images/1107f156ea3b98fb630c2bea6468a8a0fb0abccb4f4ee6b2bfa53a7f65a95c85.png

Denoising#

Common filters for denoising images are the mean filter, the median filter and the Gaussian filter.

denoised_mean = filters.rank.mean(image3.astype(np.uint8), morphology.disk(1))

plt.imshow(denoised_mean, cmap='gray')

<matplotlib.image.AxesImage at 0x12d1ba2df10>
../_images/49ec37ddeaedbcf59741d9c4dbd1ca27ead9a4a5591ea4b176600f63b44803e4.png 
denoised_median = filters.median(image3, morphology.disk(1))

plt.imshow(denoised_median, cmap='gray')

<matplotlib.image.AxesImage at 0x12d1b8ef340>
../_images/91f917f59f09e9c7c4b5409fe148b1589496cf0abf9e519bf150a28476c0076f.png 
denoised_median2 = filters.median(image3, morphology.disk(5))

plt.imshow(denoised_median2, cmap='gray')

<matplotlib.image.AxesImage at 0x12d1b96bb20>
../_images/49608828f31d0a9ab9c68428c0e09c400d3b18fa6d7d59f3b6fc80af1b78d4b6.png 
denoised_gaussian = filters.gaussian(image3, sigma=1)

plt.imshow(denoised_gaussian, cmap='gray')

<matplotlib.image.AxesImage at 0x12d1bbbb880>
../_images/6a0d5ff42a636f64e724bfd66ee0fa10fc0b35bfd20e80a8cfeb27917cae2050.png

We can also show these images side-by-side using matplotlib.

fig, axes = plt.subplots(1,3, figsize=(15,15))

axes[0].imshow(denoised_mean, cmap='gray')
axes[1].imshow(denoised_median, cmap='gray')
axes[2].imshow(denoised_gaussian, cmap='gray')

<matplotlib.image.AxesImage at 0x12d1bae6d60>
../_images/12981ee94f92a9f21e0f7c810da1d5724b2beb650430cdeca1ffc43b8acdf923.png

Top-hat filtering / background removal#

top_hat = morphology.white_tophat(image3, morphology.disk(15))

plt.imshow(top_hat, cmap='gray')

<matplotlib.image.AxesImage at 0x12d1d549c10>
../_images/ea8aef136b032c70c346c1f383994f49951670ba234c69017f4bd8d1fa4a6a77.png

Edge detection#

sobel = filters.sobel(image3)

plt.imshow(sobel, cmap='gray')

<matplotlib.image.AxesImage at 0x12d1ccc6bb0>
../_images/572e1d5995f860a01435483c2e74183d079607d0ba4481c2583c2be31ae1d99d.png

Exercise#

Apply different radii for the top-hat filter and show them side-by-side.

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