The Corsen analysis is a two steps process:
Step 2 is permormed in a independent Java based application allowing distance calculation, 3D reconstitution and basic statistical analysis. Corsen application contains 4 tabs and requires several settings described bellow.
In Corsen, the main tab is the place where informations about the current (or the last) computation is shown. The tab is composed of 3 parts:
There are 4 methods to launching a Corsen computation:
For more information about the last point, see the command line part of the documentation.
To execute the calculation of the distances, you must select input ".par" files using the menus File / Open particles A et File / Open particles B . Then you can launch the computation by pressing the Launch button. A dialog box will appear to ask you the prefix of the outputs files. Once this step is fulfilled, the computation will run.
While the computation, you can monitor the progress of Corsen with the progress bar the log on the main tab.
When the calculation is completed, the results, 3D View and History tab will be updated.
If you want to use Corsen on several images in the aim to do statistical work, it will be more convenient to use Corsen batch mode. This mode requires for each particle (A and B particles) a set of ".par" files whose names start with de same prefix. Before launching calculation, go to the Particles tab of Corsen settings and define the prefixes of the files to be traited. Then select the directory containing these files to analyze using the menu File / Open a directory , and press the launch button to run the computation.
As for a single computation all the tabs will be updated during the calculation progress.
Unlike previous methods, the visualization functionality of Corsen do not compute distances between input particles but only show the 3D visualization of the input particles. To launch this mode, follow the same steps as if you want to launch a single computation but press on 3D View instead of Launch .
The result tab presents several data about the last couple of particles that has been analyzed by Corsen. Each data can be selected using the combobox at the top of the tab and is displayed in two representations: a table and a plot. Results files (".data" and ".iv" output files) can be saved at this step if you didn't select automatic saving of output files in the settings. In the particles result sections of this tab, you can also save new ".par" files containing only some filtered particles (a filter can be set in the application settings).
| Result to display | Table description | Plot description |
|---|---|---|
| Data results summary | Statistics informations (minimum, maximum, mean, median, quartiles) about minimum distances and maximum distances. | Boxplot of minimum distances. |
| Full data results | For each center of particles B, get the intensity, minimal and maximal distances. | Histogram of the distribution of minimal distances. The number of classes of the histogram can be set in Corsen settings. |
| Intensities and distances of particles B | Show the intensity and volume for each particle B. | Plot the distribution of intensity and volumes of particles B. |
| Intensities and distances of preprocessed of particles B | Show the intensity and volume for each preprocessed of particles B. | Plot the distribution of intensity and volumes of preprocessed of particles B. |
| Intensities and distances of particles A | Show the intensity and volume for each particle A. | Plot the distribution of intensity and volumes of particles A. |
| Intensities and distances of preprocessed of particles A | Show the intensity and volume for each preprocessed of particle A. | Plot the distribution of intensity and volumes of preprocessed of particles A. |
In this tab, a 3D visualization of the last A and B analyzed particles is displayed. For each you can select several visualization mode:
In addition, two checkboxes allow the visualization of minimum calculated distances and particles barycenters. The last element of this tab is the filter view button. You can press it to open a dialog box that allows to filter the particles displayed in the 3D visualization. See the advanced topics for more information about expression filter in 3D visualization .
The History tab summaries the results of previous Corsen computations. The table shows for each previous calculation, the name of the inputs file and a result from Corsen computation that can be selected with the combobox: mean, median, min, max of the distance distributions.
The list of result type to display also includes an item called "custom". The custom statistic represents the percent of distances that pass a test whose expression is defined by the user in Corsen settings. It can be for instance the percentage of distances under a given threshold.
On the bottom of the tab you can visualize a boxplot and a histogram of the table values. The plots are drawn if there are more than 2 values in the table.
The clear button allows erasing all the results in the table for the next analysis.
The Corsen setting is a dialog box that allow users to define the behavior of Corsen. This dialog box is available in Settings > Configure Corsen... menu. To keep your changes between two Corsen launches, use the Settings > Save Settings menu.
The Corsen settings have been splited in 4 parts: Particles, Computation, Results and Visualization.
For each particle (A and B), this tab allows to set several parameters:
In addition, you can define coordinates properties on particles:
The Computation tab define properties on the number of thread to use for computation and the output files to generate.
With no threads, the distance computation will not be parallelized. In automatic mode, the number of thread to use will be the number of cores/processors available on your computer. At last, the custom field allows you to define the desired number of threads.
An option also allows to clear the result history tables before launching a batch.
This tab allows to set the number of classes for the histograms in the Results and History tab. The other field sets an optional expression for the custom statistic to display in the History tab. The expression is a Javascript expression where intensity and distance are variable for intensity and distance.