Based on MDS tutorial on his granular material labs page. This slide cover application of particle tracking: on elongated particle and biological application. Please refer to my blog for the basic of particle tracking (in Indonesian language)

1. Particle Tracking
> Elongated Particle
> Biological Application
@btatmaja

2. Simulation secret: How - to
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Run the demo program
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Error? Correct it!
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Got the exact result
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Modify the code
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Modify the math
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Improved result
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Done

3. Tracking Elongated Particles
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Introduction
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Create image with non-overlapping rectangular
particles
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Create Ideal Particle
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Calculate Least-Squares Fit Function
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Extract End Points
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Matching End Points

4. Intro - Background
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The angle of the particle is needed to determine the
position of the particle.
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Use least-squares fitting with an elongated ideal particle.
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If we knew the angle of the particle, the entire fitting
process could not be done with a single convolution
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If the angle is unknown, then many fits with ideal particles
at different angles would need to be calculated.
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The ends of long particles look more like a circle than any
other part of the particle.
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We can fit with a circle of diameter equal to the minimum
of the length and width of the object.
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This will find the two ends of the particle in one pass

5. Create image with non-overlapping
rectangular particles
20 particles of length L, width W are placed in a
NNx X NNy sized image.

6. Create Ideal Particle

7. Calculate Least-Squares Fit Function
ichi=1./chiimg(im,ip); % The inverse of the least-squares fit function is
% used since it is easier to see peaks than valleys.
simage(ichi); Title('Inverse of Least-Squares Fit Function');
colorbar;

8. Extract End Points

9. Biological Application
IDEA:
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Identify regions of the object which look more
like a circle than any other part of the object.
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We can fit with a circle at two points on the
object and extract the position and angle

10. Examine Sample Image

11. Image Correction

12. Bright Background Correction

13. Dark Background Correction I

14. Dark Background Correction II

15. Zoom in I

16. Zoom in II

17. Zoom in III

18. Looking for circle

19. Least Square Fit Function

20. Weighted Fit Function

21. Fitting to a Binary Image

22. Extract Peak Position

23. Result I

24. Result II

25. Result III – Animal tracking

26. Result IV – Zoom in X Axis

27. Result V – Head track, binary
The head track is shown for both the binary
image (blue) and the full image (green). The
binary is shifted by 10 pixels for clarity.
D
O
N
E!!