MATLAB: 2D Mask of a 3D image

image analysisimage processingImage Processing Toolbox

Hey there,

I'm rather new to using Matlab and my boss has asked me to analyze some SEM images of several membranes to compare the porosity and pore size of various membranes. The images I was given to analyze are 3D black and white images that I'd like to import into Matlab to further analyze. Ideally I'd like to be able to utilize the threshold of the image to identify the depth and thus the volume of the membrane being studied to further characterize the pores but that could be further down the road. My main question is what is the best way to create a 2D mask of the surface layer/cross-section of the image in Matlab? Also, I'd be more than happy to email a sample image if that will help clarify anything. Thanks again.

Sample Photo: https://dl.dropbox.com/u/95356349/3-009-HT-1%20T4.jpg

Best Answer

Like you said, use the threshold to identify regions of interest:

binaryImage = oneSlice > thresholdValue;

Then call do further processing or call regionprops().

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MATLAB: Extract the largest object in the RGB image

OK, if you really need to it work for a full color image, here is code for that:

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 = 22;
%--------------------------------------------------------------------------------------------------------

%    READ IN IMAGE
folder = pwd;
baseFileName = 'image.jpeg';
% 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);
% 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);
% Display the image.

hFig = figure;
subplot(2, 2, 1);
imshow(rgbImage, []);
impixelinfo;
title('Original RGB Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.

drawnow;
%--------------------------------------------------------------------------------------------------------
%    EXTRACTION OF IMAGE
% Get the max image
grayImage = min(rgbImage, [], 3);
subplot(2, 2, 2);
imshow(grayImage, []);
impixelinfo;
title('Gray Scale Image', 'FontSize', fontSize, 'Interpreter', 'None');
impixelinfo;
hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.
drawnow;
threshold = 240; % Whatever....
mask = grayImage < threshold; % Create a binary image (a mask)
% Extract the largest blob only.
mask = bwareafilt(mask, 1);
% Fill holes
mask = imfill(mask, 'holes');
% Display the image.
subplot(2, 2, 3);
imshow(mask, []);
title('Mask Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');
% Extract the individual red, green, and blue color channels.
redChannel = rgbImage(:, :, 1);
greenChannel = rgbImage(:, :, 2);
blueChannel = rgbImage(:, :, 3);
% Get the mean gray levels in R, G, and B.
meanGLR = mean(rgbImage(redChannel > threshold))
meanGLG = mean(rgbImage(greenChannel > threshold))
meanGLB = mean(rgbImage(blueChannel > threshold))
% Mask the individual color channel images.
% Make outside the mask the mean of what's above the threshold.
redChannel(~mask) = meanGLR;
greenChannel(~mask) = meanGLG;
blueChannel(~mask) = meanGLB;
% Recombine separate color channels into a single, true color RGB image.
rgbImage2 = cat(3, redChannel, greenChannel, blueChannel);
% Display the cropped image.
subplot(2, 2, 4);
imshow(rgbImage2, []);
title('Final Image', 'FontSize', fontSize, 'Interpreter', 'None');
axis('on', 'image');

MATLAB: I need to calculate certain parameters for chromosome in the image. how can i select region of chromosome alone from the background to calculate parameters.

Threshold:

binaryImage = grayImage > thresholdValue;
measurements = regionprops(binaryImage, 'all');

Best Answer

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MATLAB: Extract the largest object in the RGB image

MATLAB: I need to calculate certain parameters for chromosome in the image. how can i select region of chromosome alone from the background to calculate parameters.

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