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How do I use cross correlation to detect the Position of a particle in a stack of tiff images?

Asked by EngStudent on 31 Mar 2013

I have a project that requires me to select a region where a particle is located and than track the movement of the particle across many frames (a tiff stack). The tracking program needs to use cross correlation, I also have to plot the tracked positions. I need help developing this tracking program, any assistance will be appreciated. Thank you

0 Comments

EngStudent

1 Answer

Answer by Image Analyst on 31 Mar 2013
Edited by Image Analyst on 3 Apr 2013
Accepted answer

I'd use ginput() to have the user click on the particle. Then use normxcorr2() to find out where the particle appears in subsequent frames. Here's a demo:

% Demo to use normxcorr2 to find a template (a white onion)
% in a larger image (pile of vegetables)
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
imtool close all;  % Close all imtool figures.
clear;  % Erase all existing variables.
workspace;  % Make sure the workspace panel is showing.
format longg;
format compact;
fontSize = 20;
% Check that user has the Image Processing Toolbox installed.
hasIPT = license('test', 'image_toolbox');
if ~hasIPT
	% User does not have the toolbox installed.
	message = sprintf('Sorry, but you do not seem to have the Image Processing Toolbox.\nDo you want to try to continue anyway?');
	reply = questdlg(message, 'Toolbox missing', 'Yes', 'No', 'Yes');
	if strcmpi(reply, 'No')
		% User said No, so exit.
		return;
	end
end
% Read in a standard MATLAB color demo image.
folder = fullfile(matlabroot, '\toolbox\images\imdemos');
baseFileName = 'peppers.png';
% Get the full filename, with path prepended.
fullFileName = fullfile(folder, baseFileName);
if ~exist(fullFileName, 'file')
	% Didn't find it there.  Check the search path for it.
	fullFileName = baseFileName; % No path this time.
	if ~exist(fullFileName, 'file')
		% Still didn't find it.  Alert user.
		errorMessage = sprintf('Error: %s does not exist.', fullFileName);
		uiwait(warndlg(errorMessage));
		return;
	end
end
rgbImage = imread(fullFileName);
% Get the dimensions of the image.  numberOfColorBands should be = 3.
[rows columns numberOfColorBands] = size(rgbImage);
% Display the original color image.
subplot(2, 2, 1);
imshow(rgbImage, []);
axis on;
title('Original Color Image', 'FontSize', fontSize);
% Enlarge figure to full screen.
set(gcf, 'units','normalized','outerposition',[0 0 1 1]);
smallSubImage = imcrop(rgbImage, [192 82 60 52]);
subplot(2, 2, 2);
imshow(smallSubImage, []);
axis on;
title('Template Image to Search For', 'FontSize', fontSize);
% Search the red channel for a match.
correlationOutput = normxcorr2(smallSubImage(:,:,1), rgbImage(:,:,1));
subplot(2, 2, 3);
imshow(correlationOutput, []);
title('Normalized Cross Correlation Output', 'FontSize', fontSize);
[maxCorrValue, maxIndex] = max(abs(correlationOutput(:)));
[ypeak, xpeak] = ind2sub(size(correlationOutput),maxIndex(1));
corr_offset = [(xpeak-size(smallSubImage,2)) (ypeak-size(smallSubImage,1))];
subplot(2, 2, 4);
imshow(rgbImage);
hold on;
rectangle('position',[corr_offset(1) corr_offset(2) 60 52],...
          'edgecolor','g','linewidth',2);
title('Template Image Found in Original Image', 'FontSize', fontSize);

1 Comment

EngStudent on 2 Apr 2013

How do I retrieve the the x and y co-ordinates of the image after it has be found and detected by the cross correlation

Image Analyst

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