Mahotas – Getting Border of labels
In this article we will see how we can get the borders of the labels in the labelled image 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.labeled.borders method
Syntax : mahotas.labeled.borders(labelled_image)
Argument : It takes numpy.ndarray object as argument i.e labelled image
Return : It returns numpy.ndarray object i.e labelled image with only labels border
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 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 labelled image labeled, n_nucleus = mahotas.label(f) # showing the labelled image print ( "Labelled Image" ) imshow(labelled) show() # getting border of the labelled image relabeled = mahotas.labelled.borders(labeled) # showing the image print ( "Labels with border" ) imshow(relabelled) show() |
Output :
Example 2 :
Python3
# importing required libraries import numpy as np import mahotas from pylab import imshow, show # loading image img = mahotas.imread( 'dog_image.png' ) # filtering the image img = img[:, :, 0 ] # setting gaussian filter gaussian = mahotas.gaussian_filter(img, 15 ) # setting threshold value gaussian = (gaussian > gaussian.mean()) # creating a labelled image labelled, n_nucleus = mahotas.label(gaussian) print ( "Labelled Image" ) # showing the gaussian filter imshow(labelled) show() # getting border of the labelled image relabeled = mahotas.labelled.borders(labelled) # showing the image print ( "Labels with border" ) imshow(relabelled) show() |
Output :