Simulate image data representative of a real experiment

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As part of my research, I need to validate a particular experimental approach of image capture and particle trajectory analysis by simulating "fake" data where I have control of the parameters.
More specifically, my task is to:
  1. generate multiple particles' stochastic trajectories;
  2. create a gaussian blur of the simulated point particles, where the gaussian blur is related to the radius parameter I specifiy;
  3. discretize that gaussian-blurred particle into a grid corresponding to some pixel resolution related to the real experimental setup; and
  4. output each time step in the trajectory as a pixelated image.
I can easily complete Step 1, but my issues reside with Step 2-4. The image I've attached will hopefully provide a useful diagram that may better descripe my goal. The portion in blue is what I desire to output.
The experimental setup involves a microscope viewing top-down the trajectory of particles on a flat plane, so my "fake data" images need to represent that setup.
I've spent quite a while looking through Matlab's imaging capabilitites; however, either due to my ignorance of imaging or to my ignorance of Matlab, I have been unable to come up with an approach that meets my needs.
I appreciate any input anyone can offer.
  5 Comments
Ryan Muoio
Ryan Muoio on 5 Oct 2020
Thanks! I accepted your answer.
I'll also look into "splatting methods." I've never heard of those before. Sounds interesting.

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Accepted Answer

Bjorn Gustavsson
Bjorn Gustavsson on 3 Oct 2020
If it is enough for you to put particles at discrete pixel positions you could do something like this:
nP = 123;
dIm = spalloc(1024,1024,nP); % Or bigger if you want finer "accuracy"
x = randi(1024,[nP,1]);
y = randi(1024,[nP,1]);
dx = 7; % Just some arbitrary Gaussian widths
dy = 6; % For you to adjust
[X,Y] = meshgrid(-15:15);
fK = exp(-X.^2/dx^2-Y.^2/dy^2);
fK = fK/sum(fK(:));
Im = conv(full(dIm),fK,'same');
If you want different particles blurred with Gaussians with different widths you might get a good enough result if you separate your particles into different size-groups:
nP = [12,23,34,45,56]; % Number of particles in each group
wG = [ 2, 4, 6, 8,12]; % Gaussian 1/e half-widths in pixels
sz = [1024,1024];
Im = zeros(sz);
dIm = Im;
[X,Y] = meshgrid(-25:25);
for i1 = 1:numel(nP)
x = randi(1024,[nP(i1),1]);
y = randi(1024,[nP(i1),1]);
idx = sub2ind(sz,y,x);
dIm(idx) = 1;
fK = exp(-(X.^2+Y.^2)/wG(i1)^2);
fK = fK/sum(fK(:));
Im = Im + conv2(dIm,fK,'same');
dIm(idx) = 0;
end
This way you get some separation into different blurrings of your particles, not prefectly continuos range of sizes, but you can at least start to get some variability in, likewise you will not get particles distributed uniformly over the image field - only uniformly over the pixel centres. But this should be a simple first step. If you need you can refine this by playing tricks with distributing particles between four neighbouring pixels - or do it with more analytical aproaches (but the utility of that comes down to how well you will know the image blurring in practice...)
HTH

More Answers (1)

J. Alex Lee
J. Alex Lee on 2 Oct 2020
Bjorn's answer contains the conv2() route to blurring
fK = exp(-X.^2/dx^2-Y.^2/dy^2);
fK = fK/sum(fK(:));
Im = conv(full(dIm),fK,'same');
And if you have image processing, you could do it somewhat simpler as
Im = imgaussfilt(dIm,[dy,dx]); % or dx,dy, depending on which way is x
As for "pixelating", if you just mean binning the gray values, you could just use rounding like
s = 8; % round to nearest 6th gray value
ImP = round(Im/8)*8
  1 Comment
Ryan Muoio
Ryan Muoio on 3 Oct 2020
Thanks, J. Alex Lee! I will apply Bjorn Gustavsson's foundational code and add your pixelation idea. Hopefully, everything will work.

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