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\f0\fs24 \cf0 The tracking can be implement by running 2 routines:
\b  runSegmentCells.m
\b0  follow by 
\b runTracker.m\

\b0 Both can be found in 
\b /DATA/CellTrackerCurrent/runfiles
\b0 \
\
In more detail:\
\
There are currently two steps in the tracking/analysis:\
\
1. run runSegmentCells.m to identify nuclei and calculate fluorescence intensities. writes a mat file with the\
EDS stats structure as well as smaller peaks structure containing only the mean values. calls EDS routines\
folderFilesFromKeyword to get files and then segmentCells, addCellAvr2Stats, outputData4AWTracker. Use \
parameter files setUserParamCCC10x or setUserParamCCC20x. \
\
This routine produces a dot mat file containing the following variables:\
\

\b peaks
\b0  -- the main place the data is stored. peaks\{n\} is the data corresponding to the nth picture. Each \
row is a different cell.The columns of peaks\{n\} are:\
\
1 -- x positions\
2 -- y positions\
3 -- nuclear area\
4 -- place holder for matching index (should be a column of -1's at this point)\
5 -- mean nuclear marker intensity\
6 -- mean fluorescence intensity of smad image in the nucleus\
7 -- mean fluorescence intensity of smad image in the cytoplasm\
\

\b statsArray 
\b0 -- the direct output of EDS routine segmentCells stored for each frame. Contains more info than peaks.\
\

\b imgfiles 
\b0 -- structure array storing the names of the images used and the time of images. fields are nucfile, smadfile, time\
\

\b pictures 
\b0 -- array containing times images were taken. same as [imfiles.time]. should eventually remove for clarity but analysis routines currently use this\
\

\b userParam 
\b0 -- parameter structure used by segment cells routine\
\

\b feedings 
\b0 -- for CCC experiments, structure containing feeding times and media information.\
\

\b dateSegmentCells 
\b0 -- time the tracking was run.\
\
2. run runTracker.m to match cells from frame to frame and then assemble into single cell trajectories.\
\
This adds the following variables to the .mat file:\
\

\b cells
\b0  -- cells(n) indicates the nth cells. inside cells has two subfields:\
\
cells(n).data -- Each row represents a time points. It has the same 7 columns as peaks. \
cells(n).onframes -- list of frames in which the cell is present\
\

\b cells2 
\b0 -- this is made from cells by decideifgoodaddspline. Same as cells except can contain only a subset of the data \
(useful if problems with imaging etc) and contains additional fields:\
\
cells2(n).good 0/1 variable. it is 1 if cell meets criterion for length, smoothness etc.\
cell2.splines -- matlab splines fitting cells2.data(5:7) cell2(n).splines(1) is the spline fitting cells2(n).data(:,5)\
\
also cells2(n).data(:,8:10) contain the splines evaluated at the data points.\
\

\b peaks
\b0  -- the tracker adds two additional columns to peaks peaks\{ii\}(:,8) contains the corresponding cell numbers and peaks\{ii\}(:,9) \
contains the 0/1 flag if the cell is "good"\
\
see help for individual routines for more details and setTrackParam for parameters for these routines.\
\
3. For analysis:\
\
After the above tracking has been run, some quick plots can be made with:\
\
mkAveragePlot -- plot average flour vs time\
mksinglecellplots -- plot single cell flours vs time arrayed as subplots\
showMovieOneCell -- play movie with a cell of interest highlighted/zoomed in on. \
\
\
See also BS TrackViewer.m routine which combines much of the above analysis routines into a GUI.\
\
}