# User reviews

# Colocalization Simulator

by Thibault LagacheICY-U8L5N4

## Documentation

This plugin is designed to create two sequences with variable level of molecule colocalization.

**Image model **

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

**is equal to**

*[x,y]***I[x,y]= gain*U[x,y] + N(x,y)**

where * U* is a

*and*

**random Poisson variable***. The*

**N an additive white Gaussian noise****mean**

*λ[x,y]*of the Poisson variable*varies spatially:*

**U****,**

*λ[x,y]**=P[x,y]+B**being the*

**P[x,y]***generated in*

**sum of the intensity of the particles***and*

**[x,y]***a constant background value.*

**B***is the*

**gain=1****gain of the acquisition system**. Finally, we assumed an

*, the intensity of each particle following a spatial Gaussian distribution (*

**additive model for the intensity of the particles***).*

**Gaussian approximation of the Point Spread Function (PSF)****Parameters**

**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).**