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);
