Jeffrey Segall's Lab

Marking areas of interest in time lapse movies

Philippe Thévenaz has written a valuable series of registration plugins that can reduce/eliminate xy drift from color time lapse sequences.  This involves first downloading a plugin called TurboReg, and then downloading StackReg.  In each case, the downloads are zip files which should be extracted to the plugins folder of Image J.  The extractions will generate two folders in the plugins folder named stackReg and TurboReg.  You need to restart ImageJ, open the movie (only have 1 movie open at a time) that you would like to eliminate drift from, and then go to the plugins drop down menu in Image J, move to the Stack Reg line and click on the StackReg box that appears.  You can choose various transformations, but probably the default choice (rigid body) is best.  More information is available at the download site (http://bigwww.epfl.ch/thevenaz/stackreg/).  Note that this plugin runs quite slowly: it can easily take a minute to step through a 30 frame movie.  It registers each frame relative to the previous frame, and thus with time, black areas appear on the sides opposite the direction of drift of the movie.  The program may not be able to accommodate rapid large changes in position.  In these cases, you can use TransformJ (again available from the plugins section of the ImageJ web site) to shift sets of slices of the move in the xy plane in order to reduce the jumps enough for stack reg to track them.  Changes in z axis are extremely difficult to compensate for, requiring more extensive z series collection (perhaps every 1 – 3 um, depending on the scale of magnification) and then manually assembling images from the appropriate planes of each z series. 

Items to put in Plugins folder:

  • StackReg folder (from Thevenau web site)
  • TurboReg folder (from Thevenau web site)

Procedure

  1. Start ImageJ
  2. Open movie to be registered. 
  3. Select StackReg from plugins dropdown menu
  4. Select Rigid body transformation.
  5. Wait patiently until the progress bars in the ImageJ command bar stop appearing and the movie has stepped through all of its frames.