File of published version 1 of CellID
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Each of 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]_all_part1,
[basename]_all_part2,
[basename]_all_part3,
[basename]_all_part4,
[basename]_all_part5,
[basename]_all_part6

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

For each of the files, 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 each file are described below:

output_all:  This file contains 20 columns where 
  column 1 is the cell ID number
  column 2 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.
  column 3 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.
  column 4 and 5 are the x- and y- position, respectively, of the centroid
           of the cell,
  column 6 is the sum of the fluorescence image for all the pixels found in
           that cell
  column 7 is the area of the cell in pixels
  column 8 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)
  column 9 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.
 column 10 is the circumference of the cell in pixel units,
 column 11 and 12 are the length of the major and minor axes, respectively, 
           in pixel units
 column 13 and 14 are the total fluorescence and area of any found nucleus
           (these columns are only meaningful if there was a nuclear tagged
           image)
 column 15 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.
 column 16 is the volume of rotation of the cell around its major axis
 column 17 is the volume of the cell as determined by the "conical volume"
           method
 column 18, 19 are the vacuole area and fluorescence, respectively (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)
 column 20 is the fluorescence background level. This quantity is the mode
           of the distribution of all fluorescence pixels that are not
           associated with any cell.

file 2: output_all_part2
 This file does not contain ID, time, flag information--however, it should
 be considered as if the columns simply lay next to all the columns of
 file 1. Thus, for example, the 5th row of this file contains the information
 for the ID and time point and flag of the 5th row of the first file.

 columns 1, 2 are the fluorescence and area of all the pixels that are
           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,
 columns 3, 4 are the fluorescence and area of all pixels that are interior
           to the boundary that is one pixel smaller than the cell boundary.
 columns 5, 6 are the fluorescence and area of all pixels that are interior
           to the boundary that is two pixels smaller than the cell boundary.
 columns 7, 8 are the fluorescence and area of all pixels that are interior
           to the boundary that is three pixels smaller than the cell boundary.

file 3: output_all_part3
 This file contains information assuming that there is a third image type
 that is used to find the nucleus. As above, the columns should be considered
 as simple extensions of the columns of file 1. This file summarizes
 information from 6 ways to identify the nucleus. Columns 1-3 contain
 the fluorescence in the nuclear region from the fluorescence image, the
 fluorescence in the nucleuar region from the image that contained the 
 nuclear tag, and the area of the nuclear region, respectively, for method 1.
 The remaining columns contain the same information for methods 2 through 6
 respectively. 
 The last 6 columns where used for methods not currently implemented. There 
 value is defined to 0 for back compatibility. 

file 4: output_all_part4
 Contains the X and Y position of the found nucleus.

file 5: output_all_part5
 This file is basically more background information
 Columns 1-3 are ID number, time frame index, and flag. These should be
           identical to the same columns from file 1.

 Columns 4 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.
 column 5  is the number of pixels used in the background calculation in
           column 4
 column 6  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).
 column 7-9 contain the same information as 4-6 respectively, but instead of
           going out 5 pixels for the calculation, the number pixels outwards
           is given by half of the minor axis of the cell.

file 6: output_all_part6
 Columns 1-3 contain ID number, time, and flag
 column 4 contains a measure of surface area,
 column 5 contains the volume as measured by the "conical" volume calculation
 column 6 contains the volume as measured b the "union of spheres" method
 column 7-12 contain deprecated values.
 
 

