Icy Particle tracking benchmark generator - How generate tracks of know Diffusion coefficient

[sara...@gmail.com]

Hi

I am currently attempting to generate simulation Tracks with a known diffusion coefficient of particles. I do not quite understand how to set the parameters in the "Particle tracking benchmark generator" to this. 

If I would set a diffusion coefficient of 11 um^2/s (micrometer squared per second)  for the particles, how should I set the parameters? 

The parameters are as below when I open up the icy Particle tracking benchmark generator;

numBenchs 1
saveDir /Users/me/Desktop/benchmark
saveSequences false
displaySequences true


dim 2
seqLength 25
width 256
height 256
imageType double


numParticleGroups 1
numInitParticles 20
numNewParticlesPerFrame 1.0
pDisappear 0.05
sigma_bMax 4.0
sigma_bMin 2.0
sigma_directedMin 1.0
sigma_directedMax 2.0
vMin 2.0
vMax 4.0
p_db 0.2
p_bd 0.2
iMin 20.0
iMax 25.0


PoissonNoise false
backgroundPoisson 15.0
gain 1.0


GaussianNoise true
meanGaussian 50.0
stdGaussian 5.0

Would be great if some one could help me out! 

Thanks!

[Stephane]

Hi,

In fact you have a complete documentation about this plugin here :
http://icy.bioimageanalysis.org/plugin/Particle_tracking_benchmark_generator

You can access plugin documentation directly from the application by searching for it in the application top search bar and right clicking on a result.
Note that all parameters are expressed in pixel / frame and not um/s. Hope that help !

Best,

- Stephane