This plugin is designed to create two sequences with variable level of molecule colocalization.
We used a Mixed Poisson-Gaussian model to generate synthetic fluorescent images (see chapter 1 of the PhD thesis of N. Chenouard, Telecom Paris & Institut Pasteur). In this model, the intensity I[x,y] at pixel location [x,y] is equal to
I[x,y]= gain*U[x,y] + N(x,y)
where U is a random Poisson variable and N an additive white Gaussian noise. The mean λ[x,y] of the Poisson variable U varies spatially: λ[x,y]=P[x,y]+B, P[x,y] being the sum of the intensity of the particles generated in [x,y] and B a constant background value. gain=1 is the gain of the acquisition system. Finally, we assumed an additive model for the intensity of the particles, the intensity of each particle following a spatial Gaussian distribution (Gaussian approximation of the Point Spread Function (PSF)).
1- Syntheric image parameters
- Sequence height: Height (in pixels) of generated sequences
- Sequence width: Width (in pixels) of generated sequences
- Sequence length: Time length of generated sequences. Spot positions are independent from each other between images at different time points.
- Number of Spots 1: Number of spots in each image of the first sequence. Spot positions are uniformly distributed.
- Number of Spots 2: Number of spots in each image of the first sequence. Spot positions (that do not colocalize!) are uniformly distributed.
- Min. Spot Intensity/Max. Spot Intensity: Min/Max. intensity of spots (the intensity of each spot is uniformly distributed between min. and max.)
- Mean Gaussian noise: Mean value of the additive Gaussian noise N (see model above)
- Poisson noise: Background value B of the Poisson noise (see model above)
2- Colocalization parameters
- Percentage of colocalization: Percentage of spots 2 that colocalize with spots 1
- Mean distance of colocalization: Mean distance between colocalized spots: The distance between the center of mass of 2 colocalized spots is modeled with a Gaussian variable (Thomas process).
- Std. distance of colocalization: Standard deviation of the distance between colocalized spots: The distance between the center of mass of 2 colocalized spots is modeled with a Gaussian variable (Thomas process).