I just wanted to ask if you can give a brief tutorial on how to use the TrackMate plugin. Specifically, I am interested in using it to track movement of live cells captured through bright field time-lapse microscopy. So I wanted to know if you can just go through the steps on how I can select manually the cells I want to track, but have to plugin track the cells I select automatically. Currently I am using manual tracking to track the cells, but it is very time consuming. Thanks for your help!
you can start TrackMate via Plugins > Tracking > TrackMate and select Manual annotation in the second step of the wizard. Continue to the viewer selection and select the default Hyperstack Displayer. After you have done that, you can create spots manually (see http://imagej.net/Manual_tracking_with_TrackMate#Creating_spots_one_by_one for details). Subsequent steps concern the tracking and use your previously added spots.