MATLAB: How to use cross correlation to detect the Position of a particle in a stack of tiff images

frame trackingImage Processing Toolboxregion selectiontracking using cross correlation

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

Best 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);
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