Mahotas – Filtering Labels

In this article we will see how we can filter the labels of the labelled image in mahotas. Filtering label is similar to implementing the relabeling feature but the difference is in filtering we will remove i.e filter the labels at the time of calling the filtering method and filtering will give us new labeled image and number of labels. We use mahotas.label method to label the image

For this we are going to use the fluorescent microscopy image from a nuclear segmentation benchmark. We can get the image with the help of command given below

mhotas.demos.nuclear_image()

Below is the nuclear_image

Labeled images are integer images where the values correspond to different regions. I.e., region 1 is all of the pixels which have value 1, region two is the pixels with value 2, and so on

In order to do this we will use mahotas.label.filter_labeled method



Syntax : mahotas.label.filter_labeled(label_image, filter1, filter2)

Argument : It takes labeled image object and filters as argument

Return : It returns the labelled image and integer i.e number of labels

Note : Filters can be border label filter, maximum size anything.

Example 1:

filter_none

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# importing required libraries
import mahotas
import numpy as np
from pylab import imshow, show
import os
  
# loading nuclear image
f = mahotas.demos.load('nuclear')
  
# setting filter to the image
f = f[:, :, 0]
  
# setting gaussian filter
f = mahotas.gaussian_filter(f, 4)
  
# setting threshold value
f = (f> f.mean())
  
# creating a labeled image
labeled, n_nucleus = mahotas.label(f)
  
# printing number of labels
print("Count : " + str(n_nucleus))
  
# showing the labeleed image
print("Labelled Image")
imshow(labeled)
show()
  
  
# filtering the label image
# adding border filter
relabeled, n_left = mahotas.labeled.filter_labeled(labeled, remove_bordering = True)
  
# showing number of labels
print("Count : " + str(n_left))
  
# showing the image
print("No border Label")
imshow(relabeled)
show()

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Output :

Example 2:

filter_none

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# importing required libraries
import mahotas
import numpy as np
from pylab import imshow, show
import os
  
# loading nuclear image
f = mahotas.demos.load('nuclear')
  
# setting filter to the image
f = f[:, :, 0]
  
# setting gaussian filter
f = mahotas.gaussian_filter(f, 4)
  
# setting threshold value
f = (f> f.mean())
  
# creating a labeled image
labeled, n_nucleus = mahotas.label(f)
  
# printing number of labels
print("Count : " + str(n_nucleus))
  
# showing the labeleed image
print("Labelled Image")
imshow(labeled)
show()
  
  
# filtering the label image
# adding max size filter
relabeled, n_left = mahotas.labeled.filter_labeled(labeled, max_size = 7000)
  
# showing number of labels
print("Count : " + str(n_left))
  
# showing the image
print("Max size 7000 Label")
imshow(relabeled)
show()

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Output :




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