Input particles can be filtered by setting with an expression the "filter" fields for particles A and B in the "Particles" tab in Corsen Settings.
The expression must use the Javascript syntax. Several variable are defined for the test:
| Variable name | Comment |
|---|---|
| area | Area of the particle |
| density | Density of the particle |
| intensity | Intensity of the particle |
| sphericity | Sphericity of the particle |
| volume | Volume of the particle |
Here an example:
intensity > 10000 && volume > 30
Unlike the filtering of input particles, the filtering of particle in the 3D visualization is set by pressing on "Filter" button in the 3D View tab.
The expression system is the same as in the previous topic,except the name of the variable for filtering distances (see table below). For particles A and B, use the previously described variables.
| Variable name | Comment |
|---|---|
| distance | Distance (can be negative) between a particle A and a particle B |
| area | Area of the particle |
| density | Density of the particle |
| intensity | Intensity of the particle |
| sphericity | Sphericity of the particle |
| volume | Volume of the particle |
Sample of expression :
distance>1 && distance < 3
Different biological localization issue can be tackle by Corsen thanks to several distance calculation options that should be chosen depending on the shape of objects to be analyzed.
Please, before starting Corsen analysis carefully consider these different options.
You should keep in mind that distances will be always calculated from particles A archors to particles B archors and that these archors will be defined by the selected particles processing option (see table below).
Corsen is a very flexible tool, you can select a particle type in order to choose the algorithm used in the distances computation. The following table summary the characteristics of the available particles type.
| Particle type | Example | Particles A archors used to compute distances | Particles B archors used to compute distances |
|---|---|---|---|
| All points particle | Any object | All the points of the particles | All the points of the particles |
| Barycenter particle | Any object | Barycenters of the particles | Barycenters of the particles |
| Decomposition particle | RNAm | Barycenter of particles preprocessed in cuboids | All the points of the particle preprocessed in cuboids |
| Surface particle | Nucleus, mitochondria | All the points of the cuboids that are at the surface of the particles | All the points of the cuboids that are at the surface of the particles. If the archor of particles A is in a particle B, the distance will be negative |
If you want to add another type of particle, you can do it by adding your particle type to Corsen source code. See the download source section to download Corsen source code and see compiling instructions.
The current generation of processors often contains two or mores core that allow to do easily parallel computations. Corsen can take usage of the many core to increase the speed of distance computation. By default no thread are used to compute the distance, you can enable it in the computation tab of Corsen setting. If you choose to set the number of threads to automatic, this number will be equals to the number of processors/cores in your computer.