How to get all yellow piexels that interact with the blue piexels?

Hello everybody,

I have one image that was plotted by imagesc. I need to get all yellow piexels that close to the blue piexels. I have indicated them in the figure. The value of blue piexel is 0. I can use it to filter the piexels. But I am not sure how to write this code. Any ideas? I have attched the code and data.

figure(1)

min1=0;
max1=100;
data = load('myFile.txt');
imagesc(data)
xlabel('X (\mum)','FontName','Times New Roman','FontSize',14);
ylabel('Y (\mum)','FontName','Times New Roman','FontSize',14);
caxis([min1 max1]);
colorbar;

Thanks,

MCC

Answer 1

[Image Analyst]

Try this, using bwboundaries() from the Image Processing Toolbox:

% Demo 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.)
clearvars;
workspace;  % Make sure the workspace panel is showing.
format short g;
format compact;
fontSize = 14;

figure(1)

min1=0;
max1=100;
data = load('myFile.txt');
subplot(3, 1, 1);
imagesc(data)
hold on;
xlabel('X (\mum)','FontName','Times New Roman','FontSize',fontSize);
ylabel('Y (\mum)','FontName','Times New Roman','FontSize',fontSize);
caxis([min1 max1]);
colorbar;
axis('on', 'image');
impixelinfo
subplot(3, 1, 2);
histogram(data, 32);
grid on;
title('Histogram','FontSize',fontSize);
xlabel('Data Value','FontSize',fontSize);
ylabel('Count','FontSize',fontSize);

% Create a mask so we can get the boundaries of it.
mask = data > 50;
subplot(3, 1, 3);
imshow(mask);
title('Mask','FontSize',fontSize);

% Plot the borders of all the blobs in the overlay above the original grayscale image 
% using the coordinates returned by bwboundaries().
% bwboundaries() returns a cell array, where each cell contains the row/column coordinates for an object in the image.
imshow(data); % Optional : show the original image again.  Or you can leave the binary image showing if you want.
% Here is where we actually get the boundaries for each blob.
boundaries = bwboundaries(mask);
% boundaries is a cell array - one cell for each blob.
% In each cell is an N-by-2 list of coordinates in a (row, column) format.  Note: NOT (x,y).
% Column 1 is rows, or y.    Column 2 is columns, or x.
numberOfBoundaries = size(boundaries, 1); % Count the boundaries so we can use it in our for loop
% Here is where we actually plot the boundaries of each blob in the overlay.
hold on; % Don't let boundaries blow away the displayed image.
for k = 1 : numberOfBoundaries
	thisBoundary = boundaries{k}; % Get boundary for this specific blob.
	x = thisBoundary(:,2); % Column 2 is the columns, which is x.
	y = thisBoundary(:,1); % Column 1 is the rows, which is x.
	% First plot over original.
	subplot(3, 1, 1);
	plot(x, y, 'r-', 'LineWidth', 2); % Plot boundary in red.
	% Next plot over bottom mask image.
	subplot(3, 1, 3);
	plot(x, y, 'r-', 'LineWidth', 2); % Plot boundary in red.
end
hold off;
caption = sprintf('%d Outlines, from bwboundaries()', numberOfBoundaries); 
title(caption, 'FontSize', fontSize); 
axis('on', 'image'); % Make sure image is not artificially stretched because of screen's aspect ratio.
% Maximize window
g = gcf;
g.WindowState = 'maximized'
fprintf('Done running %s.m\n', mfilename);fprintf('Done running %s.m\n', mfilename);

[MCC]

Thanks a lot. This answer solved my problem.

Answer 2

[darova]

What about contour?

[m,n] = size(data);
[x,y] = meshgrid(1:m,1:n);
[C,h] = contour(x,y,data,[0.9 0.9]);
h1 = get(h,'children');
x1 = get(h1(1),'xdata');
y1 = get(h1(1),'ydata');
plot(x1,y1)

[MCC]

Hi darova,

I tried your code. But it gave me errors. The error messag is: The size of X must match the size of Z or the number of columns of Z. Then I transpose data the code becomes this:

[m,n] = size(data);
[x,y] = meshgrid(1:m,1:n);
[C,h] = contour(x,y,data',[0.9 0.9]); % data has been transposed
h1 = get(h,'children');
x1 = get(h1(1),'xdata');
y1 = get(h1(1),'ydata');
plot(x1,y1)

It gave me error again: Index exceeds array bounds. Not sure not happned. Thanks.

Thanks,

MCC

[darova]

Which line throws an error?

[MCC]

Index exceeds array bounds.

Error in MarginCapture (line 5)

x1 = get(h1(1),'xdata');