Applying the same mask on a set of images

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Elliza Feisol 2020-7-14

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https://ww2.mathworks.cn/matlabcentral/answers/564896-applying-the-same-mask-on-a-set-of-images

评论： Image Analyst 2020-7-14

I would like to apply a mask on the channels (semicircles) so it can be excluded from analysis of cell distribution (figure attached). I am required to apply a mask for 120 images, is it possible to read and write as well as apply the mask to all 120 images?

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Answer 1

Image Analyst 2020-7-14

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https://ww2.mathworks.cn/matlabcentral/answers/564896-applying-the-same-mask-on-a-set-of-images#answer_465659

Yes. See code samples in the FAQ: https://matlab.fandom.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F

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Image Analyst 2020-7-14

在 MATLAB Online 中打开

If you need help on the masking part, see this:

% Code to mask out white semicircles in the image.
% By Image Analyst
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 = 15;
%--------------------------------------------------------------------------------------------------------
%    READ IN IMAGE
folder = pwd;
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
grayImage = imread(fullFileName);
% 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(grayImage);
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(grayImage);
	% 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 = grayImage(:, :, 1); % Take red channel.
end
% Crop it to the right lines.
% grayImage = grayImage(1750:2250, 800:end);
subplot(2, 2, 1);
imshow(grayImage, []);
impixelinfo;
title('Red Channel Image', 'FontSize', fontSize, 'Interpreter', 'None');
hFig = gcf;
hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.
drawnow;
subplot(2, 2, 2);
imhist(grayImage);
grid on;
title('Histogram of Original Image', 'FontSize', fontSize, 'Interpreter', 'None');
%--------------------------------------------------------------------------------------------------------
%    SEGMENTATION OF IMAGE
% Get a binary image by interactively thresholding using the function at
% https://www.mathworks.com/matlabcentral/fileexchange/29372-thresholding-an-image
% 128 seems good for this image.
lowThreshold = 128;
highThreshold = 255;
% [lowThreshold, highThreshold] = threshold(lowThreshold, highThreshold, grayImage)
mask = grayImage > lowThreshold & grayImage < highThreshold;
mask = imfill(mask, 'holes');
% Take 4 largest blobs.
mask = bwareafilt(mask, 4);
subplot(2, 2, 3);
imshow(mask, []);
impixelinfo;
caption = sprintf('Mask of White SemiCircles');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
% Mask the image
grayImage(mask) = 0;
% Display the masked image.
subplot(2, 2, 4);
imshow(grayImage, []);
impixelinfo;
caption = sprintf('Masked Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
hFig = gcf;
hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.
drawnow;

Elliza Feisol 2020-7-14

Thank you for your help. I have tried applying the code, however, the mask of white semcircles does not appear and the image is not masked. Is there any way to fix this issue?

Image Analyst 2020-7-14

I had cropped the images because I assumed you didn't really have that big white frame around everything. If you really have that, then delete the call to imclearborder() and pass 1 into bwareafilt() instead of 4.

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