hello I am new to MATLAB and I faced this problem as a university project I have to find circles the original image had really poor lighting I got this result after pre processing. now I have problem detecting circles and tracking them.its a stack (.tif) 200 images and particles have a different location in each image. is there any code out there or any algorithm can help me in this project?
MATLAB: Finding circles and tracking
detecting circles find circlesImage Processing Toolbox
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Try this demo. Adapt as needed, like to change the input filename:
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 = 15;%===============================================================================
% Read in gray scale demo image.
% Let's let the user select from a list of all the demo images that ship with the Image Processing Toolbox.
folder = fileparts(which('cameraman.tif')); % Determine where demo folder is (works with all versions).
baseFileName = 'cameraman.tif';% 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; endendrgbImage = imread(fullFileName);% Display the image.
subplot(2, 2, 1);imshow(rgbImage, []);title('Original Grayscale Image', 'FontSize', fontSize, 'Interpreter', 'None');axis('on', 'image');hp = impixelinfo();% 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)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(rgbImage);
% 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 = rgbImage(:, :, 2); % Take green channel.
else grayImage = rgbImage; % It's already gray scale.
end% Now it's gray scale with range of 0 to 255.
%------------------------------------------------------------------------------
% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0, 0.04, 1, 0.96]);% 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.
set(gcf, 'Name', 'Demo by ImageAnalyst', 'NumberTitle', 'Off')drawnow;% Make a mask for the top half of the image
binaryImage = false(rows, columns);binaryImage(1 : round(rows/2), 1 : columns) = true;% Display the image.subplot(2, 2, 2);imshow(binaryImage, []);title('Upper half mask', 'FontSize', fontSize, 'Interpreter', 'None');axis('on', 'image');% Use it to zero out the other parts of the image.
grayImage(~binaryImage) = 0;% Display the image.subplot(2, 2, 3);imshow(grayImage, []);title('Masked gray image', 'FontSize', fontSize, 'Interpreter', 'None');axis('on', 'image');hp = impixelinfo();%------------------------------------------------------------------------------% Measure blobs
props = regionprops(binaryImage, grayImage, 'WeightedCentroid');xy = props.WeightedCentroid% Put a red cross at the centroid.
hold on;plot(xy(1), xy(2), 'r+', 'MarkerSize', 100, 'LineWidth', 3);% Update title
caption = sprintf('Centroid at x (column) = %.1f, y (row) = %.1f', xy(1), xy(2));title(caption, 'FontSize', fontSize, 'Interpreter', 'None');
Use regionprops():
% Code to detect angle of a blob.
% By Image Analyst
clc; % Clear the command window.
fprintf('Beginning to run %s.m ...\n', mfilename);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 = 15;%--------------------------------------------------------------------------------------------------------
% READ IN IMAGE
folder = pwd;baseFileName = 'ZoomIn_100f.jpg';% 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; endendgrayImage = 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(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% Crop it to the right lines.
% grayImage = grayImage(1750:2250, 800:end);
subplot(2, 2, 1);imshow(grayImage, []);impixelinfo;title('Red Channel Image', 'FontSize', fontSize, 'Interpreter', 'None');hFig = gcf;hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.
drawnow;subplot(2, 2, 2);imhist(grayImage);grid on;title('Histogram of Original Image', 'FontSize', fontSize, 'Interpreter', 'None');%--------------------------------------------------------------------------------------------------------% SEGMENTATION OF IMAGE
% Get a binary image by interactively thresholding using the function at
% https://www.mathworks.com/matlabcentral/fileexchange/29372-thresholding-an-image
% 91 seems good for this image.
lowThreshold = 91;highThreshold = 255;% [lowThreshold, highThreshold] = threshold(lowThreshold, highThreshold, grayImage)
mask = grayImage > lowThreshold & grayImage < highThreshold;mask = imclearborder(mask);mask = imfill(mask, 'holes');% Take largest blobs.
mask = bwareafilt(mask, 1);subplot(2, 2, 3);imshow(mask, []);impixelinfo;caption = sprintf('Mask of White SemiCircles');title(caption, 'FontSize', fontSize, 'Interpreter', 'None');% Measure centroid and orientation.
props = regionprops(mask, 'Centroid', 'Orientation')xCenter = props.Centroid(1);yCenter = props.Centroid(2);hold on;plot(xCenter, yCenter, 'r+', 'MarkerSize', 40, 'LineWidth', 2);% Display the masked image.
subplot(2, 2, 4);overlayImage = imoverlay(grayImage, mask, 'r');imshow(overlayImage, []);impixelinfo;caption = sprintf('Masked Image. Angle = %.2f degrees.', props.Orientation);title(caption, 'FontSize', fontSize, 'Interpreter', 'None');hFig = gcf;hFig.WindowState = 'maximized'; % May not work in earlier versions of MATLAB.drawnow;% Make a line at that angle at the centroid.
slope = tan(props.Orientation)x = 1 : columns;y = slope * (x - xCenter) + yCenter;hold on;plot(x, y, 'r-', 'LineWidth', 2);fprintf('Done running %s.m ...\n', mfilename);
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