Table 14.18.1.

Cell-ID Output Variables

Variable Name		Description
General measurements
1	pos	Position number (i.e., id of image field); same for a single cell through every set of images of a time course. This variable is created by Rcell when the dataset is loaded.
2	cellID	Cell identification number. In FRET experiments the cells in the upper and lower part of the split image are differentiated by an offset of 1000 added to this value.
3	ucid	Unique cell id. A variable that identifies cells across different positions; defined as pos*offset+cellID, where offset is 100000. This variable is created by Rcell when the dataset is loaded.
4	t.frame	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.
5	time	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 (only meaningful if using Metamorph images).
6	xpos	x coordinate of the centroid of the cell
7	ypos	y coordinate of the centroid of the cell
8	f.tot	Sum of the fluorescence image for all the pixels found in that cell
9	a.tot	Area of the cell in pixels
10	fft.stat	Statistic derived from the one-dimensional fast-Fourier-transform (FFT) of the function: radius vs. angle, where the radius is the distance from the cell centroid to the boundary at a given angle. Its value is the root of the squared sum of the ratio FFT(ω)/FFT(0) over all ω>0; for a perfect circle FFT_stat is 0, and we interpret this statistic as a measure of non-circularity.
11	perim	Circumference of the cell in pixel units
12	maj.axis	Length of the major axis in pixel units
13	min.axis	Length of the minor in pixel units
14	flag	Indicates the image type. For example, for 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
15	rot.vol	Volume of rotation of the cell around its major axis
16	con.vol	Volume of the cell as determined by the conical volume method (Gordon et al., 2007)
17	a.vacuole	Vacuole area: calculated from the region inside the cell that is less brightly fluorescent. In exponentially growing cells expressing fluorescence localized to the cytoplasm, this “dark” region corresponds to the vacuole.
18	f.vacuole	Vacuole fluorescence: calculated from the region inside the cell that is less brightly fluorescent. In exponentially growing cells expressing fluorescence localized to the cytoplasm, this “dark” region corresponds to the vacuole.
19	f.bg	Fluorescence background level; the mode of the distribution of all fluorescence pixels not associated with any cell
To calculate membrane proximal fluorescence (for relocalization experiments)
20	f.tot.p1	Fluorescence of all the pixels interior to the boundary that is one pixel wider than the cell boundary. Numbers thus include the original cell plus an annular region one pixel around the outside of the cell.
21	a.tot.p1	Area of all the pixels interior to the boundary that is one pixel wider than the cell boundary. Numbers thus include the original cell plus an annular region one pixel around the outside of the cell.
22	f.tot.m1	Fluorescence of all pixels interior to the boundary that is one pixel smaller than the cell boundary
23	a.tot.m1	Area of all pixels interior to the boundary that is one pixel smaller than the cell boundary
24	f.tot.m2	Fluorescence of all pixels interior to the boundary that is two pixels smaller than the cell boundary
25	a.tot.m2	Area of all pixels interior to the boundary that is two pixels smaller than the cell boundary
26	f.tot.m3	Fluorescence of all pixels interior to the boundary that is three pixels smaller than the cell boundary
27	a.tot.m3	Area of all pixels interior to the boundary that is three pixels smaller than the cell boundary
Information obtained from the “nuclear image” type (Variables contain the area and fluorescence of concentric disks of user-defined radius.)
28	f.nucl	Total fluorescence in the found nucleus. To find the nucleus, Cell-ID moves a disc with a radius of two pixels around the interior of the cell and finds the location where the disc has the maximum total fluorescence. From that location it calculates the fluorescence within a circle of four pixels of radius. This process is done for every fluorescence image. If some pixels of the disc fall outside the cell boundary, they are not used in the quantification.
29	a.nucl	Area of the found nucleus
30	f.nucl1 to f.nucl6	Same as f.nucl, but using a disc of increasing radius to calculate the fluorescence for each image. f.nucl1 uses a disc of 2 pixels of radius, f.nucl2 uses a disc of 3 pixels, and so forth up to f.nucl6 which uses a disc of 7 pixels of radius.
31	a.nucl1 to a.nucl6	The area corresponding to f.nucl1 to f.nucl6
32	f.nucl.tag1 to f.nucl.tag6	Same as f.nucl1 to f.nucl6, but the fluorescence is calculated from the nuclear tagged fluorescent channel, specified in step 15b. If no nuclear channel is specified, these variables are equal to f.nucl1 to 6.
More background information
33	f.local.bg	Measure of the background level at pixels located 5 radial pixels further out than the cell boundary; thus, a measure of the local fluorescence background level, the average fluorescence per pixel. Only pixels along the annular boundary NOT associated with ANY cell are included; background level here is the mean of the pixels.
34	a.local.bg	The number of pixels used in the background calculation for local.bg
35	a.local	Total number of pixels along the annular region, including all pixels (i.e., pixels associated with cells and pixels not associated with any cell)
36	f.local2.bg a.local2.bg a.local2	Same information as the previous three variables, but using the background level at pixels located x radial pixels outward of the cell boundary, where x is one half of the minor axis of the cell.
More volume measurements
37	a.surf	Surface area as calculated by the union of spheres method (Gordon et al., 2007)
38	sphere.vol	Volume a measured by the union of spheres method (Gordon et al., 2007)