How to remove the pectoral muscle from the mammogram?

Question

Afaf Saad 2018-9-10

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https://ww2.mathworks.cn/matlabcentral/answers/418369-how-to-remove-the-pectoral-muscle-from-the-mammogram

编辑： Image Analyst 2022-5-15

I used imclearborder() but it doesn’t work. Can anyone give me advice?! i want to remove the left part behind the red line

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Afaf Saad 2018-9-10

编辑：Afaf Saad 2018-9-10

在 MATLAB Online 中打开

yes, pectoral muscle removal is the second step i want to do because i want to train Convolution neural network with those images after getting ROI. i extracted the whole breast but i want to remove this part to improve the segmented images. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%555 clc;

    close all
    clear;
   %load image from my directory
    folder='C:\Users\afaf\Documents\MATLAB\all-mias\NormaL';
    newfolder='C:\Users\afaf\Documents\MATLAB\all-mias\NormalRotated';
    filepattern=fullfile(folder,'*.pgm');
    myfiles=dir(filepattern);
    se = strel('disk',15);
    % read images and resize
    for k=1:length(myfiles)
         images{k}=imread(myfiles(k).name);
         images{k} = imresize(images{k},[224 224]);
    %to extract the whole breast
         BW1 = imbinarize(images{k});
         nhood = true(9);
         closeBW1 = imclose(BW1,nhood);
         roughMask = imfill(closeBW1,'holes');
         BW2 = bwareafilt(roughMask,1);
         I2=images{k};
         I2(~BW2)=0;
         images{k}=I2;
         temp=images{k};
       %normalize the image
         images{k}=temp-min(temp(:))/max(temp(:))-min(temp(:));
         images{k}=adapthisteq(images{k});
         baseFileName = sprintf('Image #%d.png', k);
         fullFileName = fullfile(newfolder, baseFileName);
         imwrite(images{k}, fullFileName);
%%%%%
end

Afaf Saad 2018-9-10

it already works, just extracting the whole breast and getting rid of the tags. he didn't mention extra process to do.

Afaf Saad 2018-9-10

what is your opinion ?

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Answer 1

Image Analyst 2018-9-10

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/418369-how-to-remove-the-pectoral-muscle-from-the-mammogram#answer_336213

testGrayImage.m

See attached demo.

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Image Analyst 2022-5-12

在 MATLAB Online 中打开

@AHT.fatima I don't think that is robust. See my new code below, which is more robust. It deletes any bright blob in the upper right or upper left corner.

@Afaf Saad

The problem is you're dealing with a screenshot rather than the original image. I've made a few changes to just crop the image to what you'd have if you had the original image.

clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clearvars;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
folder = pwd;
baseFileName = 'mammo B5.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, 3, 1);
imshow(rgbImage, []);
title('Original RGB Screenshot Image', 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo;
axis('on', 'image'); % Make sure image is not artificially stretched because of screen's aspect ratio.
% Get the dimensions of the image.
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
grayImage = rgbImage; % Initialize.
[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
% The image is not the original image - it's a screenshot that has a white frame around it.
% Get rid of white frame and crop image.
grayImage = grayImage(55:1078, 183:951);
% Update image size.
[rows, columns, numberOfColorChannels] = size(grayImage);
% Display the image.
subplot(2, 3, 2);
imshow(grayImage, []);
hp = impixelinfo;
title('Cropped Gray Scale Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image'); % Make sure image is not artificially stretched because of screen's aspect ratio.
%------------------------------------------------------------------------------
% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0, 0.04, 1, 0.96]);
drawnow;
% Display the histogram.
subplot(2, 3, 3);
imhist(grayImage);
grid on;
title('Histogram of Gray Scale Image', 'FontSize', fontSize, 'Interpreter', 'None');
% Turn into a binary image to get the pectoral muscle.
lowThreshold = 130;
highThreshold = 255;
% https://www.mathworks.com/matlabcentral/fileexchange/29372-thresholding-an-image?s_tid=srchtitle
% [lowThreshold, highThreshold] = threshold(lowThreshold, highThreshold, grayImage)
binaryImage = grayImage > lowThreshold & grayImage <= highThreshold;
% Display the binary image.
subplot(2, 3, 4);
imshow(binaryImage, []);
caption = sprintf('Bright Regions Mask Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo;
axis('on', 'image'); % Make sure image is not artificially stretched because of screen's aspect ratio.
drawnow;
% Extract only blob in the upper left or upper right corners.
pectMask = bwselect(binaryImage, 1, 1) | bwselect(binaryImage, columns, 1);
% Fill holes
binaryImage = imfill(pectMask, 'holes');
% Display the binary image.
subplot(2, 3, 5);
imshow(pectMask, []);
caption = sprintf('Pectoral Mask Image');
title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
hp = impixelinfo;
axis('on', 'image'); % Make sure image is not artificially stretched because of screen's aspect ratio.
drawnow;
% Erase the gray scale image there.
grayImage(pectMask) = 0;
% Display the masked image.
subplot(2, 3, 6);
imshow(grayImage);
axis('on', 'image'); % Make sure image is not artificially stretched because of screen's aspect ratio.
caption = sprintf('Image with Pectoral Muscle Masked out.');
title(caption, 'FontSize', fontSize);
drawnow;

AHT.fatima 2022-5-15

removal of PM.m

hello everyone, can someone explain this code to me please .... it gives me good results but I did not understand its principle (by the way it is a code for the removal of the pectoral muscle after binarization)...

Image Analyst 2022-5-15

编辑：Image Analyst 2022-5-15

I did explain my code, in the comments. Nearly every small snippet of code is explained. Which comment don't you understand? I don't know who wrote that code that you attached. You'd have to ask them if you'd rather use their code than mine. I really don't have time to re-write their code correctly, like by adding in the code missing from the beginning to read in the images and assign variables, put in the missing comments, etc.

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How to remove the pectoral muscle from the mammogram?

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How to remove the pectoral muscle from the mammogram?

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