This is an archive of the old MediaWiki-based ImageJ wiki. The current website can be found at

MSER as the segmentation method

After making this choice of segmentation in the advanced mode the following panel appears


Here the user can again make a choice of increasing or decreasing the edge enhancement factor. All the MSER parameters appear here in the second panel, read more about MSER parameters. After making suitable parameter selection the user can then go over the tracking options where they can see some advanced parameter selections for the optimizer and assignment layer of the program. This panel is shown here


Read more about sub-pixel localization parameter selection.

  • Start tracking

If the user does not wish to change the default settings for sub-pixel localization, they can skip this step and directly click on start tracking button to start the tracking from user defined first and last frame.

  • Save parameters

After successful tracking, the user has the option to save the program parameters, so that the movie can be run (again) in batch mode. This choice can also be made without doing the tracking after just making the parameter selection. Clicking on this button triggers the close of the program and saves the program parameters in IJ.log file of FIJI, this close of program is done to ensure that the log file is properly updated by FIJI.