Quickstart Guide

Corsen plug-in


To install the ImageJ plug-in, go to the Corsen website main page and download the plug-in jar archive.

Then put this jar file in your ImageJ plug-in folder (usually C:\Program Files\ImageJ\plugins on Microsoft Windows).

Analysis process

Now, you can launch ImageJ. Open the image to analysis by Corsen (You can find samples files (images and .par files) in the samples section of the documentation ). Note that with Corsen, only image stacks are handled.

Define a threshold on your image stack ( Image > Adjust > Threshold menu or Ctrl+Shift+T shortcut).

You can now run The Corsen ImageJ plug-in ( Plugins > Analyze > Corsen Plugin ).

The Corsen plug-in setup menu will appear, check options that you want. See the plug-in documentation for more informations. Press OK to launch the analysis.

A Warning dialog ask you to process all the images in the stack, answer Yes .

According the checked options, a "Save as" dialog can appear at the end of the process. If everything worked properly, a ".par" file will be generated and saved in the same directory as the processed image. Sample ".par" files can be found in Corsen handbook .

Corsen application

Launch Corsen application

The Corsen application is a Java Web Start application, so to launch it, you only have to click on the link (in orange) on the Corsen website.

After few seconds, the application will appear. During the first launch (and after each Corsen update), a message will ask you to validate the security certificates of the application.

Loading par files

First, select the first input file ( File > Open Particle A ).

Then select the second input file ( File > Open Particle B ).

At each time, the information box is updated :

Then launch the computation of the distances by pressing Launch .

A dialog box, will ask you for the name of the output files prefix.

While Corsen process data, you can follow the computational steps thanks to a progress bar and a log. A message will inform you when the calculation process is completed.

The result tab

The result tab shows informations about the particles and the distances calculated by Corsen for the last couple of particles.

The 3D visualization

Corsen includes a 3D visualization interface in which calculated distances are shown together with the input particles.

The history tab

For all the previous computation, some characteristic data of the calculated distance distribution are collected in the history table. It can be median, minimal, maximal distance or, depending on the user settings, the percentage of particles under a given distance threshold. You can also get statistics on all the recorded results.

Process all the particles of a directory

Run Corsen for many couples for particle, can be tedious, so you can run Corsen on a batch of files. To do that you must define the prefix for each type of particles in the setting:

Then select the directory containing the files to process ( File > Open a directory... ):

At last, launch the process as usual.