Applying the same mask on a set of images

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?

Answer 1

[Image Analyst]

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

[Image Analyst]

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]

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]

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.