Image manipulation in Matlab

a = double(imread('figures_from_microscope/500nm_particles_1200.tif'));
colormap('gray'), imagesc(a);

b = bpass(a,0,5,20);
#    bpass(img,lnoise, lobject, threshold)
colormap('gray'), image(b);

pk = pkfnd(b,25,3);
#     pkfnd(im, th, sz)

fid = fopen('exp.txt', 'w');
fprintf(fid, '%6.2f %12.8f\n', pk);
fclose(fid);

pk= pkfnd(b(200:400,200:400), 30,10);

# Below is a way to display multiple figures
figure(1); colormap('gray'), imagesc(a);
figure(2); colormap('gray'), image(b);
figure(3); colormap('gray'), image(b(200:400,200,400));
figure(4); colormap('gray'), image(a(200:400,200:400));

# This will put dots of 'r'ed on the particles of interest.
plot(pk(:,1),pk(:,2),'r.')
Looking at a small section of an image and checking for accuracy of the image manipulation is necessary. This is important since we make many assumptions on what particles to look at and what to ignore [this is what values in bpass and pkfnd do].

If var is a variable you are using in Matlab, it can be saved into a file using:
save('filename.txt', 'var', '-ascii')

These are the relevant links:
http://physics.georgetown.edu/matlab/tutorial.html
http://www.physics.emory.edu/~weeks/idl/tracking.html
http://www.physics.emory.edu/~weeks/idl/index.html