Mahotas – Getting Border of label at given region

In this article we will see how we can get the border of the label in the labelled image within the given region in mahotas. 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

In order to do this we will use mahotas.labeled.border method

Syntax : mahotas.labeled.border(labeled_image, i, j)

Argument : It takes numpy.ndarray object i.e labelled image and two integer as argument
Note : A pixel is on the border if it has value i (or j)



Return : It returns numpy.ndarray object i.e labeled image with border label

Note : The input of the this should should be the filtered image object which is labeled
In order to filter the image we will take the image object which is numpy.ndarray and filter it with the help of indexing, below is the command to do this

iamge = image[:, :, 0]

Example 1 :

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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)
  
  
# showing the labeleed image
print("Labelled Image")
imshow(labeled)
show()
  
# getting border for label at given point
relabeled = mahotas.labeled.border(labeled, 0, 20)
  
# showing the image
print("Labels With borders at given point")
imshow(relabeled)
show()

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Output :

Example 2 :

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# importing required libraries
import numpy as np
import mahotas
from pylab import imshow, show
   
# loading iamge
img = mahotas.imread('dog_image.png')
     
# filtering the imagwe
img = img[:, :, 0]
      
# setting gaussian filter
gaussian = mahotas.gaussian_filter(img, 15)
   
# setting threshold value
gaussian = (gaussian > gaussian.mean())
   
# creating a labeled image
labeled, n_nucleus = mahotas.label(gaussian)
    
print("Labelled Image")
# showing the gaussian filter
imshow(labeled)
show()
   
# getting border for label at given point
relabeled = mahotas.labeled.border(labeled, 1, 0)
  
# showing the image
print("Labels With borders at given point")
imshow(relabeled)
show()

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Output :




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