File of version 1.2a of CellID
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The output files are text files containing information about each cell
found in each time point. A brief desription of each column in these files
is contained here. The names of the files are
[basename]_all
[basename]_img


where [basename] is the determined by the user when cell was run. Here we
assume that [basename] is given by the word "output"

For output_all, each row contains the information for a given cell
at a given time point and a given fluorescence type (as determined by the
"flag" variable). The columns of the file are described below:

output_all:  This file contains 61 columns where 

  cellID   is the cell ID number

  t.frame  is the time frame of the cell (0 through n-1 where n=number of
           points in the time course). Not every cell is necessarily found
           in every time point.

  time     is the time of that time frame in seconds. The time unit is an
           absolute number of seconds from some time in the distance past,
           but the time elapsed between time frames is more meaningful.

  xpos     is the x- position, of the centroid of the cell,
  ypos     is the y- position, of the centroid of the cell,

  f.tot    is the sum of the fluorescence image for all the pixels found in
           that cell
  a.tot    is the area of the cell in pixels

  num.pix  is the number of pixels associated with the cell (column 7 and 8
           are identical but were not originally identical as column 7
           in an earlier version of the code tried to correct for the pixelated
           cell boundaries)

  fft.stat is "FFT_stat" This statistic is derived from the one dimensional
           fast-fourier-transform of the function radius vs angle, where
           radius is the distance from the cell centroid to the boundary at
           a given angle. FFT_stat is 1 minus the ratio of the magnitude
           squared of the 0th order component to the sum of the magnitude
           squared of all other components. For a perfect circle FFT_stat is
           0, and we interpret this statistic as a measure of circularity.

 perim     is the circumference of the cell in pixel units,

 maj.axis  is the length of the major axe, in pixel units
 min.axis  is the length of the minor axe, in pixel units

 f.nucl    the total fluorescence of any found nucleus
 a.nucl    the total area (in pixel units) of any found nucleus
           (these last two columns are only meaningful if there was a nuclear 
	   tagged image)

 flag      is "flag" This indicates the "image type." Thus if there are
           for example YFP and CFP images, all YFP images would be flag 0 and
           all CFP would be flag 1, assuming that the YFP image was
           taken earliest in time.

 rot.vol   is the volume of rotation of the cell around its major axis
 con.vol   is the volume of the cell as determined by the "conical volume"
           method

 a.vacuole is the vacuole area (in pixel units)
 f.vacuole is the vacuole fluorescence
	   (these are calculated by looking for darker regions of fluorescence 
	   within the cell and should be ignored if that information would not be
           meaningful for a given experiment)

 f.bg      is the fluorescence background level. This quantity is the mode
           of the distribution of all fluorescence pixels that are not
           associated with any cell.

 f.tot.p1  are the fluorescence and area of all the pixels that are
 a.tot.p1  interior to the boundary that is one pixel wider than the cell
           boundary. These numbers thus include the original cell plus 
           an annular region one pixel around the outside of the cell,

 f.tot.m1  are the fluorescence and area of all pixels that are interior
 a.tot.m1  to the boundary that is one pixel smaller than the cell boundary.
 
 f.tot.m2  are the fluorescence and area of all pixels that are interior
 a.tot.m2  to the boundary that is two pixels smaller than the cell boundary.
 
 f.tot.m3  are the fluorescence and area of all pixels that are interior
 a.tot.m3  to the boundary that is three pixels smaller than the cell boundary.

 The next 20 columns contain information of the nucleus fluorescence. The nucleus
 is found by maximizing the fluorescence in a disc of defined radius (nucleus_radius_1,
 default to 2px). The fluorescence in concentric discs of defined radius (nucleaus_radius_1
 to nucleus_radius_6) is calculated. The nucleus is searched in each channel and this value
 is kept in f.nucl1 to f.nucl6 
 If a channel is specified as "nuclear tag" when executing Cell-ID, it is used
 to find the nucleus. The other channels nuclear fluorescence is calculated 
 from the nuclear areas defined by the nuclear tag channel. This information is
 kept in f.nucl.tag1 to f.nucl.tag6. If no "nuclear tag" channel is specified, f.nucl.tag
 is equivalent to f.nucl
	
 xpos.nucl	the x position of the found nucleus
 ypos.nucl	the y position of the found nucleus
 f.nucl1 	the fluorescence in the nuclear region from the fluorescence image.
 f.nucl.tag1  	the fluorescence in the nucleuar region found in the nuclear tag image.
 a.nucl1  	the area of the nuclear region.

 The remaining 21 columns contain the same information for methods 2 through 8 
 respectively.

 local.bg  	is a measure of the background level at pixels located 5 radial
           	pixels further out than the cell boundary. It is thus a measure
           	of the local fluorescence background level. The background level
           	is the average fluorescence per pixel. For this calculation only
           	pixels along the annuluar boundary that are not associated with any
           	cell are included. The background level here is the mean of the
           	pixels.
 local.bg.num 	is the number of pixels used in the background calculation in
           	column 4
 local.num   	is the total number of pixels along the annular region, including
           	all pixels (which means pixels associated with a cell and pixels
           	not associated with any cell).
 
 local2.bg 	contain the same information as the 3 previous columns, but instead 
 local2.bg.num  of going out 5 pixels for the calculation, the number pixels outwards
 local2.num     is given by half of the minor axis of the cell.

 a.surf 	contains a measure of surface area,
 con.vol 	contains the volume as measured by the "conical" volume calculation
 sphere.vol	contains the volume as measured b the "union of spheres" method

 
 

