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
mahotas.demos.nuclear_image()
Below is the nuclear_image
In order to do this we will use mahotas.labelled.border method
Syntax : mahotas.labelled.border(labelled_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 labelled image with border label
Note : The input of the this should be the filtered image object which is labelled
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
image = image[:, :, 0]
Example 1 :
Python3
# importing required librariesimport mahotasimport numpy as npfrom pylab import imshow, showimport os# loading nuclear imagef = mahotas.demos.load('nuclear')# setting filter to the imagef = f[:, :, 0]# setting gaussian filterf = mahotas.gaussian_filter(f, 4)# setting threshold valuef = (f> f.mean())# creating a labelled imagelabelled, n_nucleus = mahotas.label(f)# showing the labelled imageprint("Labelled Image")imshow(labelled)show()# getting border for label at given pointrelabeled = mahotas.labelled.border(labelled, 0, 20)# showing the imageprint("Labels With borders at given point")imshow(relabelled)show() |
Output :
Example 2 :
Python3
# importing required librariesimport numpy as npimport mahotasfrom pylab import imshow, show # loading imageimg = mahotas.imread('dog_image.png') # filtering the imageimg = img[:, :, 0] # setting gaussian filtergaussian = mahotas.gaussian_filter(img, 15) # setting threshold valuegaussian = (gaussian > gaussian.mean()) # creating a labelled imagelabelled, n_nucleus = mahotas.label(gaussian) print("Labelled Image")# showing the gaussian filterimshow(labelled)show() # getting border for label at given pointrelabeled = mahotas.labelled.border(labelled, 1, 0)# showing the imageprint("Labels With borders at given point")imshow(relabelled)show() |
Output :
