MATLAB: How to remove irregular shaped cells in this image

Question

I want to remove the cells which are not in regular shape like the ones marked in the image. Can anyone help me with this. Thanks in advance.

Answer 1

OK, here, try this, adjusting thresholding parameters as needed.

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
% Check that user has the specified Toolbox installed and licensed.
hasLicenseForToolbox = license('test', 'image_toolbox');   % license('test','Statistics_toolbox'), license('test','Signal_toolbox')
if ~hasLicenseForToolbox
  % User does not have the toolbox installed, or if it is, there is no available license for it.
  % For example, there is a pool of 10 licenses and all 10 have been checked out by other people already.
  ver % List what toolboxes the user has licenses available for.
  message = sprintf('Sorry, but you do not seem to have the Image Processing Toolbox.\nDo you want to try to continue anyway?');
  reply = questdlg(message, 'Toolbox missing', 'Yes', 'No', 'Yes');
  if strcmpi(reply, 'No')
    % User said No, so exit.
    return;
  end
end
%===============================================================================
% Read in gray scale demo image.
folder = pwd; % Determine where demo folder is (works with all versions).
baseFileName = 'image.png';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
  % The file doesn't exist -- didn't find it there in that folder.  
  % Check the entire search path (other folders) for the file by stripping off the folder.
  fullFileNameOnSearchPath = baseFileName; % No path this time.
  if ~exist(fullFileNameOnSearchPath, 'file')
    % Still didn't find it.  Alert user.
    errorMessage = sprintf('Error: %s does not exist in the search path folders.', fullFileName);
    uiwait(warndlg(errorMessage));
    return;
  end
end
rgbImage = imread(fullFileName);
% Display the image.





subplot(2, 2, 1);
imshow(rgbImage, []);
title('Original Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis on;
hp = impixelinfo();
% Get the dimensions of the image.  
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
[rows, columns, numberOfColorChannels] = size(rgbImage);
if numberOfColorChannels > 1
  % It's not really gray scale like we expected - it's color.
  % Use weighted sum of ALL channels to create a gray scale image.
%   grayImage = rgb2gray(rgbImage); 
  % ALTERNATE METHOD: Convert it to gray scale by taking only the green channel,
  % which in a typical snapshot will be the least noisy channel.
  grayImage = rgbImage(:, :, 1); % Take red channel.
else
  grayImage = rgbImage; % It's already gray scale.
end
% Display the image.
subplot(2, 2, 1);
imshow(grayImage, []);
title('Gray Scale Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis on;
%------------------------------------------------------------------------------
% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0, 0.04, 1, 0.96]);
% Get rid of tool bar and pulldown menus that are along top of figure.
% set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off') 
% Get binary image.
binaryImage = grayImage > 10;
% Get rid of white frame.
binaryImage = imclearborder(binaryImage);
% Display the image.
subplot(2, 2, 1);
imshow(binaryImage, []);
title('Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis on;
% Fill holes
binaryImage = imfill(binaryImage, 'holes');
% Display the image.
subplot(2, 2, 2);
imshow(binaryImage, []);
title('Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis on;
% Let's measure things to see what we're starting with.
props = regionprops(binaryImage, 'Solidity', 'Area', 'perimeter');
allAreas = [props.Area]
allSolidities = [props.Solidity]
allCircularities = 4 * pi * allAreas ./ [props.Perimeter] .^ 2
% Display the histograms.
subplot(2, 2, 3);
histogram(allSolidities);
grid on;
title('Histogram of Solidities', 'FontSize', fontSize, 'Interpreter', 'None');
subplot(2, 2, 4);
histogram(allCircularities);
grid on;
title('Histogram of circularities', 'FontSize', fontSize, 'Interpreter', 'None');
% Take the 24 smoothest blobs.
% Get rid of blobs less solid than 0.85%.
binaryImage2 = bwpropfilt(binaryImage, 'Solidity', [.85, inf]);
figure;
% Display the image.
subplot(2, 1, 1);
imshow(binaryImage2, []);
title('Binary Image2 - high solidity', 'FontSize', fontSize, 'Interpreter', 'None');
axis on;
% Get rid of blobs with low circularity.
highCircularityIndexes = find(allCircularities > 0.6);
labeledImage = bwlabel(binaryImage);
binaryImage3 = ismember(labeledImage, highCircularityIndexes);
% Display the image.
subplot(2, 1, 2);
imshow(binaryImage3, []);
title('Binary Image3 - high circularity', 'FontSize', fontSize, 'Interpreter', 'None');
axis on;