How to use plugin (Main menu)
After installation of plugin it will appear in the Analyze submenu of ImageJ (not Plugins):
By clicking on it plugin's main menu with most common tasks will be shown:
Typical workflow is following: open your image/movie with single molecules and start with Detect Molecules option. Plugin will detect and fit particles on image and compile results in Results table that will be shown in the end of the detection\analysis.
To build superresolution image use Reconstruct Image menu. It will render all detected localizations using Results table. The last one is usual ImageJ table and can be stored as tab-separated values, saved, loaded, modified, etc.
Drift Correction module will use cross-correlation function to correct for possible drift of microscope's stage during acquisition. It can be stored and loaded later using Load and Apply Drift Correction menu.
Link Particles function will use detection results to construct tracks from particles' localization at different frames. These results can be used to load/save your tracks in MTrackJ plugin format for further editing.
Sort Results will sort columns of Results table in ascending or descending order (I'm surprised ImageJ cannot do it on its own).
Last two menus "Load" and "Save" particles in "old DoM format" intended for reverse compatibility with previous versions of plugin.
Here is list of links to wiki pages with detailed description of each function: