%    Copyright (C) 2005
%    Geoff Gordon  ggordon@cs.cmu.edu
%    Andrew Gove
%
%    This file is part of DotTrack, dot tracking software for
%    fluorescence microscope images.
%
%    DotTrack is free software; you can redistribute it and/or modify
%    it under the terms of the GNU General Public License as published
%    by the Free Software Foundation; either version 2 of the License,
%    or (at your option) any later version.
%
%    This program is distributed in the hope that it will be useful,
%    but WITHOUT ANY WARRANTY; without even the implied warranty of
%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
%    General Public License for more details.
%
%    You should have received a copy of the GNU General Public License
%    along with this program; if not, write to the Free Software
%    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
%    02110-1301 USA

DotTrack is dot tracking software for fluorescence microscope images.
There are two versions, one which tracks two points using single 2-D
slices (or z-projections) from each frame of a 2- or 3-D movie, and
one which tracks 1-4 points using full 3-D information.  Either
version is started by executing the file run.m in the appropriate
directory, either TwoD or ThreeD.

To use this software, you will need to edit the file run.m in the
appropriate directory to include the input pathname for your movie.  A
movie is stored as a bunch of images with related filenames.  Each
filename contains a frame ID and a slice ID; different slices of the
same frame are combined into a 3d stack, and then different frames are
processed in order to make the whole movie.

For example, the call

movie = loadmovie('/home/ggordon/data/im%02d_z%02d.tif',1:15,1:5);

inside run.m would load the movie to be processed from the directory
'/home/ggordon/data/'.  A typical file in this directory would have a
name like 'im03_z01.tif'.  This file corresponds to slice 1 of frame 3
of the movie.  There are 15 frames in all (numbered 1:15), and each
frame has five slices (numbered 1:5).

If you give the TwoD version a movie with more than one z-slice per
frame, it will use the z-projection for tracking.  You can tell it to
use just one slice by specifying that slice in the last argument of
loadmovie; e.g. 7 would specify only the seventh slice.
