How to impose Binary mask on rgb color image

Hi i have threshold a rgb color image into binary image.

Now i want to impose this image onto my original image to get the purple cells and rest of the image remains black. Anyone have idea? Thanks a lot.

[Khajista Nizam]

rgbimage=imread('original image'); %upload your original image b=binarymask; %Your binary mask

%Change the dimension of the binary mask to match with the original image >>bIn3Dims = repmat(b,1,1,3); R = rgbimage(:, :, 1); G = rgbimage(:, :, 2); B = rgbimage(:, :, 3);

%zero will keep the background black. Write 255 if you want it to be white R(~b) = 0; G(~b) = 0; B(~b) = 0; blackBG = cat(3, R, G, B); figure; imshow(blackBG);

Answer 1

[Image Analyst]

To mask an RGB image with a binary/logical image, simply do this:

% Mask the image using bsxfun() function
maskedRgbImage = bsxfun(@times, rgbImage, cast(mask, 'like', rgbImage));

[Sarmad Shafique]

It gives the below error. Kindly help me regarding this. Thanks

Error using bsxfun Non-singleton dimensions of the two input arrays must match each other.

Error in Untitled (line 4) maskedRgbImage = bsxfun(@times, RGB, cast(mask, 'like', RGB));

[Image Analyst]

Like it says, the size of the mask must be the same as your image. How many rows and columns do your mask and image have? Evidently, they're different!

[Canberk Suat Gurel]

Hello Image Analyst,

My mask is

My rgbImage is

and the result is

So, why is it not working? Thanks!

[Image Analyst]

Your mask is not binary. It's showing severe jpeg artifacts. It may even be color or uint8. You need to make it a binary image:

mask = mask(:,:,1) > 128;

Never us jpeg images for image analysis - that changes the pixel values. Use PNG or some other non-compressed form (TIFF, BMP, etc.) but never jpeg.

[W.Khan]

Hello Image Analyst! Thanks for your great work here. What if we only want the masked area on the RGB image. I mean overlay the mask on the RGB and delete/discard the rest of the image except the masked area?

[Image Analyst]

Khan, Canberk, Sarmad, and others: Attached is a full demo. Adapt as needed.

% Demo to find buns leaving the oven.  By Image Analyst, Sep 26, 2020.
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clearvars;
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 16;
fprintf('Beginning to run %s.m ...\n', mfilename);

%-----------------------------------------------------------------------------------------------------------------------------------
% Read in image.
folder = [];
baseFileName = 'cells.jpeg';
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
% It's not an RGB image!  It's an indexed image, so read in the indexed image...
rgbImage = imread(fullFileName);
[rows, columns, numberOfColorChannels] = size(rgbImage)
% Display the test image.
subplot(2, 2, 1);
imshow(rgbImage, []);
axis('on', 'image');
caption = sprintf('Image : "%s"', baseFileName);
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo(); % Set up status line to see values when you mouse over the image.

% Set up figure properties:
% Enlarge figure to full screen.
hFig1 = gcf;
hFig1.Units = 'Normalized';
hFig1.WindowState = 'maximized';
% 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.
hFig1.Name = 'Demo by Image Analyst';

mask = imread('mask.jpeg');
[rowsm, columnsm, numberOfColorChannelsm] = size(mask)
mask = mask(:,:,1) > 128; % Convert to binary.
if rows ~= rowsm || columns ~= columnsm
	% Resize mask to match image.
	mask = imresize(mask, [rows, columns], 'Nearest');
end
% Display the initial mask image.
subplot(2, 2, 2);
imshow(mask, []);
hp = impixelinfo(); % Set up status line to see values when you mouse over the image.
axis('on', 'image');
title('Mask', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;

% Mask the image using bsxfun() function to multiply the mask by each channel individually.  Works for gray scale as well as RGB Color images.
maskedRgbImage = bsxfun(@times, rgbImage, cast(mask, 'like', rgbImage));

% Display the final masked image.
subplot(2, 2, 3);
imshow(maskedRgbImage, []);
axis('on', 'image');
title('Masked Image', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo(); % Set up status line to see values when you mouse over the image.

% Display the final masked image of the background by inverting the mask.
% Mask the image using bsxfun() function to multiply the mask by each channel individually.  Works for gray scale as well as RGB Color images.
backgroundImage = bsxfun(@times, rgbImage, cast(~mask, 'like', rgbImage));
subplot(2, 2, 4);
imshow(backgroundImage, []);
axis('on', 'image');
title('Background Image', 'FontSize', fontSize, 'Interpreter', 'None');
drawnow;
hp = impixelinfo(); % Set up status line to see values when you mouse over the image.

[jacques Ben bilombe]

Thank you for the script

Answer 2

[Jan]

RGB  = rand(640, 480, 3);  % Test data
mask = rand(640, 480) > 0.2;

mask3 = cat(3, mask, mask, mask);
RGBm  = RGB;
RGBm(mask3) = 0;

[Sarmad Shafique]

Hi Sir Jan Simon! thanks for answering, will you please elaborate this code. For example if the threshold image is 'threshold.jpg' and color image is 'rgbcolor.jpg'. Then how we will write this code to get results. Thanks a lot!

[Jan]

Is "threshold.jpg" a RGB image?

[Marco Andres Acevedo Zamora]

Hello, for a more personalised pixel color on the replacement use (adjust the code to your variable names):

 bw = (slide_clahe_sp(:, :, 1) == 255) | ...
            (slide_clahe_sp(:, :, 2) == 255) | ...
             (slide_clahe_sp(:, :, 3) == 255);
        mask = cat(3, bw, bw, bw);
        available = size(bw_oversaturated_red(mask), 1);
        v = zeros(available, 1);
        intervals = available/3:available/3:available+1;
        v(1:intervals(1)) = 255; %R
        v(intervals(1):intervals(2)) = 0; %G
        v(intervals(2):intervals(3)) = 0; %B

This way, you will have a red pixel whenever the 3 dimensional mask is true. It is useful for highlighting oversaturated pixels like the tool available on the optical microscopy software Element NIS-BR. Cheers,