The clist data file

The clist file has two matrices : clist.data and clist.data3D.

The clist.data matrix stores single-value (non-time dependent) information about the cells, e.g. mean fluorescence, number of neighbors at birth, birth time, long axis length at birth etc. It can be used to gate cells on specific parameters without having to load every cell file, but can also be used for visualizing single value information for your dataset. An individual clist is stored in each xy directory.

The initial clist quantities stored can be obtained by typing clist.def’.

Here is what is currently in the clist :

'1 : Cell ID'
'2 : Region Num birth'
'3 : Region Num death'
'4 : Cell birth Time'
'5 : Cell Division Time'
'6 : Cell Age'
'7 : Old Pole Age'
'8 : Error Frame'
'9 : stat0'
'10 : Long axis (L) birth'
'11 : Long Axis (L) death'
'12 : Short Axis birth'
'13 : Short Axis death'
'14 : Area birth'
'15 : Area death'
'16 : Region Score birth'
'17 : Region Score death'
'18 : x position birth'
'19 : y position birth'
'20 : fluor1 sum'
'21 : fluor1 mean'
'22 : fluor2 sum'
'23 : fluor2 mean'
'24 : Num of neighbors'
'25 : Region gray val'
'26 : Focus1(1) long axis birth'
'27 : Focus1(1) short axis birth'
'28 : Focus1(1) score birth'
'29 : Focus1(1) intensity birth'
'30 : Focus1(2) long axis birth'
'31 : Focus1(2) short axis birth'
'32 : Focus1(2) score birth'
'33 : Focus1(2) intensity birth'
'34 : Focus1(3) long axis birth'
'35 : Focus1(3) short axis birth'
'36 : Focus1(3) score birth'
'37 : Focus1(3) intensity birth'
'38 : Focus1(4) long axis birth'
'39 : Focus1(4) short axis birth'
'40 : Focus1(4) score birth'
'41 : Focus1(4) intensity birth'
'42 : Focus1(5) long axis birth'
'43 : Focus1(5) short axis birth'
'44 : Focus1(5) score birth'
'45 : Focus1(5) intensity birth'
'46 : Focus1(1) long axis pole align'
'47 : Focus1(1) long axis norm pole align'
'48 : Focus1(1) long axis normalized'
'49 : Focus1(2) long axis normalized'
'50 : Focus1(3) long axis normalized'
'51 : Focus1(4) long axis normalized'
'52 : Focus1(5) long axis normalized'
'53 : Focus1(1) short axis normalized'
'54 : Focus1(2) short axis normalized'
'55 : Focus1(3) short axis normalized'
'56 : Focus1(4) short axis normalized'
'57 : Focus1(5) short axis normalized'
'58 : Focus1(1) gaussianFitWidth'
'59 : Focus1(2) gaussianFitWidth'
'60 : Focus1(3) gaussianFitWidth'
'61 : mother ID'
'62 : daughter1 ID'
'63 : daughter2 ID'
'64 : dL max'
'65 : dL min'
'66 : L death / L birth'
'67 : fluor1 sum death'
'68 : fluor1 mean death'
'69 : fluor2 sum death'
'70 : fluor2 mean death'
'71 : Focus1(1) long axis death'
'72 : Focus1(1) short axis death'
'73 : Focus1(1) score death'
'74 : Focus1(1) intensity death'
'75 : Focus1(2) long axis death'
'76 : Focus1(2) short axis death'
'77 : Focus1(2) score death'
'78 : Focus1(2) intensity death'
'79 : Focus1(2) long axis death'
'80 : Focus1(3) short axis death'
'81 : Focus1(3) score death'
'82 : Focus1(3) intensity death'
'83 : Focus1(4) long axis death'
'84 : Focus1(4) short axis death'
'85 : Focus1(4) score death'
'86 : Focus1(4) intensity death'
'87 : Focus1(5) long axis death'
'88 : Focus1(5) short axis death'
'89 : Focus1(5) score death'
'90 : Focus1(5) intensity death'
'91 : Focus1(1) gaussian fit width death'
'92 : Focus1(2) gaussian fit width death'
'93 : Focus1(3) gaussian fit width death'
'94 : long axis/short axis birth'
'95 : long axis/short axis death'
'96 : Neck Width'
'97 : Maximum Width'
'98 : Cell Dist to edge'
'99 : Generation'
'100 : Generation0'
'101 : Progenitor'
'102 : Growth Rate'

For a more detailed description of each of these values, please see the Cell Descriptors List at the end of this page.

The clist.data3D or Time-Clist is a 3D matrix which contains [Cells x 3DClist Dimension x Time frames]. It contains a quantity for each cell and each time frame. Examples of quantities included are average fluorescence, long axis length, area. The names of the fields can be found under clist.def3d'.

CELL DESCRIPTORS LIST

'1 : Cell ID' - This is a unique ID number assigned by SuperSegger to each identified cell in a dataset

'2 : Region Num birth' - Identification number assigned by SuperSegger to the region of this cell in "Cell Birth Time" frame

'3 : Region Num death' - Identification number assigned by SuperSegger to the region of this cell in "Cell Divsion Time" frame

'4 : Cell birth time' - The frame number in which the cell is born. This will be frame 1 if the cell was already present in the first frame, and therefore will be 1 for all cells in a snapshot experiment.

'5 : Cell death time' - The frame number in which the cell is last identified, either due to division, death (lysis) or the end of the dataset. If the cell was present in the final frame, this will be the last frame. It will therefore be 1 for all cells in a snapshot experiment.

'6 : Cell Age' - The number of frames in which the cell "lived" or was identified. This if simply the difference between the cell division and birth times (plus one).

'7 : Old Pole Age' - Number of generations the old pole of a cell has existed

'8 : Error Frame' - The first frame in which SuperSegger has an error for this cell

'9 : stat0' - Indicator of cell birth and death. stat0 = 0 means no birth was observed, stat0 =1 means no death/division was observed , stat0 = 2 means both birth and death were observed.

'10 : Long Axis' - Length of the long axis of the cell in the "Cell Birth Time" frame

'11 : Long Axis death' - Length of the long axis of the cell in the "Cell Division Time" frame

'12 : Short Axis birth' - Length of the short axis of the cell in the "Cell Birth Time" frame

'13 : Short Axis death' - Length of the short axis of the cell in the "Cell Division Time" frame

'14 : Area birth' - Area of the cell in the "Cell Birth Time" frame

'15 : Area death' - Area of the cell in the "Cell Division Time" frame

'16 : Region Score birth' - Score assigned by SuperSegger for the region of this cell in "Cell Birth Time" frame

'17 : Region Score death' - Score assigned by SuperSegger for the region of this cell in "Cell Birth Time" frame

'18 : x position birth' - Pixel number along the x axis for the center of the cell in the "Cell Birth Time" frame

'19 : y position birth' - Pixel number along the y axis for the center of the cell in the "Cell Birth Time" frame

'20 : fluor1 sum' - Fluorescence intensity integrated over the cell area for the Channel 1 Fluorescence in "Cell Birth Time" frame

'21 : fluor1 mean' - Average (by area) fluorescence intensity for the cell for the Channel 1 Fluorescence in "Cell Birth Time" frame

'22 : fluor2 sum' - Fluorescence intensity integrated over the cell area for the Channel 2 Fluorescence in "Cell Birth Time" frame

'23 : fluor2 mean' - Average (by area) fluorescence intensity for the cell for the Channel 2 Fluorescence in "Cell Birth Time" frame

'24 : Number of neighbors' - Number of other cells with boundaries touching this cell's boundary

'25 : Region gray val' - Brightfield intensity value for the region of this cell

'26 : Focus1(1) longaxis' - Long axis position of the brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'27 : Focus1(1) shortaxis'- Short axis position of the brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'28 : Focus1(1) score' - Score assigned by focus identifier for brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'29 : Focus1(1) Intensity' - Intensity of the brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'30 : Focus1(2) longaxis' - Long axis position of the 2nd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'31 : Focus1(2) shortaxis' - Short axis position of the 2nd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'32 : Focus1(2) score' - Score assigned by focus identifier for 2nd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'33 : Focus1(2) Intensity' - Intensity of the 2nd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'34 : Focus1(3) longaxis' - Long axis position of the 3rd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'35 : Focus1(3) shortaxis' - Short axis position of the 3rd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'36 : Focus1(3) score'- Score assigned by focus identifier for 3rd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'37 : Focus1(3) Intensity' - Intensity of the 3rd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'38 : Focus1(4) longaxis' - Long axis position of the 4th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'39 : Focus1(4) shortaxis' - Short axis position of the 4th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'40 : Focus1(4) score'- Score assigned by focus identifier for 4th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'41 : Focus1(4) Intensity' - Intensity of the 4th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'42 : Focus1(5) longaxis' - Long axis position of the 5th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'43 : Focus1(5) shortaxis' - Short axis position of the 5th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'44 : Focus1(5) score'- Score assigned by focus identifier for 5th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'45 : Focus1(5) Intensity' - Intensity of the 5th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'46 : Focus1(1) longaxis pole_align' - Long axis position of the brightest focus in Fluorescence Channel 1, with cell oriented by old pole/new pole in "Cell Birth Time" frame

'47 : Focus1(1) longaxis normalized pole_align' - Long axis position normalized to cell length of the brightest focus in Fluorescence Channel 1, with cell oriented by old pole/new pole in "Cell Birth Time" frame

'48 : Focus1(1) longaxis normalized' - Long axis position normalized to cell length of the brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'49 : Focus1(2) longaxis normalized' - Long axis position normalized to cell length of the 2nd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'50 : Focus1(3) longaxis normalized' - Long axis position normalized to cell length of the 3rd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'51 : Focus1(4) longaxis normalized' - Long axis position normalized to cell length of the 4th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'52 : Focus1(5) longaxis normalized' - Long axis position normalized to cell length of the 5th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'53 : Focus1(1) shortaxis normalized' - Short axis position normalized to cell length of the brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'54 : Focus1(2) shortaxis normalized' - Short axis position normalized to cell length of the 2nd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'55 : Focus1(3) shortaxis normalized' - Short axis position normalized to cell length of the 3rd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'56 : Focus1(4) shortaxis normalized' - Short axis position normalized to cell length of the 4th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'57 : Focus1(5) shortaxis normalized' - Short axis position normalized to cell length of the 5th brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame

'58 : Focus1(1) gaussianFitWidth' - Width of the Gaussian fit to the brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame in "Cell Birth Time" frame

'59 : Focus1(2) gaussianFitWidth' - Width of the Gaussian fit to the 2nd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame in "Cell Birth Time" frame

'60 : Focus1(3) gaussianFitWidth' - Width of the Gaussian fit to the 3rd brightest focus in Fluorescence Channel 1 in "Cell Birth Time" frame in "Cell Birth Time" frame

'61 : mother ID' - "Cell ID" of this cell's mother cell (the cell which divided to give birth to this cell)

'62 : daughter1 ID' - "Cell ID" of one daughter cell (cell formed through this cell's division)

'63 : daughter2 ID' - "Cell ID" of second daughter cell (cell formed through this cell's division)

'64 : dl max' - Maximum change in long axis length in a single frame during this cell's lifetime

'65 : dl min' - Minimum change in long axis length in a single frame during this cell's lifetime

'66 : l/l_birth' - Ratio of long axis lengths in "Cell Division Time" frame and "Cell Birth Time" frame

'67 : fluor1 sum death' - Fluorescence intensity integrated over the cell area for the Channel 1 Fluorescence in "Cell Division Time" frame

'68 : fluor1 mean death' - Mean (by area) fluorescence intensity for the cell for the Channel 1 Fluorescence in "Cell Division Time" frame

'69 : fluor2 sum death' - Fluorescence intensity integrated over the cell area for the Channel 2 Fluorescence in "Cell Division Time" frame

'70 : fluor2 mean death' - Mean (by area) fluorescence intensity for the cell for the Channel 2 Fluorescence in "Cell Division Time" frame

'71 : Focus1(1) longaxis death' - Long axis position of the brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'72 : Focus1(1) shortaxis death' - Short axis position of the brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'73 : Focus1(1) score death' - Score assigned by focus identifier for brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'74 : Focus1(1) Intensity death' - Intensity of the brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'75 : Focus1(2) longaxis death' - Long axis position of the 2nd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'76 : Focus1(2) shortaxis death' - Short axis position of the 2nd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'77 : Focus1(2) score death' - Score assigned by focus identifier for 2nd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'78 : Focus1(2) Intensity death' - Intensity of the 2nd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'79 : Focus1(2) longaxis death' - Long axis position of the 3rd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'80 : Focus1(3) shortaxis death' - Short axis position of the 3rd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'81 : Focus1(3) score death' - Score assigned by focus identifier for 3rd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'82 : Focus1(3) Intensity death' - Intensity of the 3rd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'83 : Focus1(4) longaxis death' - Long axis position of the 4th brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'84 : Focus1(4) shortaxis death' - Short axis position of the 4th brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'85 : Focus1(4) score death' - Score assigned by focus identifier for 4th brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'86 : Focus1(4) Intensity death' - Intensity of the 4th brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'87 : Focus1(5) longaxis death' - Long axis position of the 5th brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'88 : Focus1(5) shortaxis death' - Short axis position of the 5th brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'89 : Focus1(5) score death' - Score assigned by focus identifier for 5th brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'90 : Focus1(5) Intensity death' - Intensity of the 5th brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'91 : Focus1(1) gaussianFitWidth death' - Width of the Gaussian fit to the brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'92 : Focus1(2) gaussianFitWidth death' - Width of the Gaussian fit to the 2nd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'93 : Focus1(3) gaussianFitWidth death' - Width of the Gaussian fit to the 3rd brightest focus in Fluorescence Channel 1 in "Cell Division Time" frame

'94 : long axis/short axis birth' - Ratio of long to short axis lengths in "Cell Birth Time" frame

'95 : long axis/short axis death' - Ratio of long to short axis lengths in "Cell Division Time" frame

'96 : Neck Width' - Shortest short axis width found along the length of the cell

'97 : Maximum Width' - Longest short axis width found along the length of the cell

'98 : Cell Dist to edge' - Distance from cell center to edge of frame

'99 : Generation' - cell generation tracked (w/o error) progenitor can originate in any frame.

'100 : Generation0' - cell generation tracked (w/o error) progenitor can originate only in first frame.

'101 : Progenitor' - progenitor cell ID

'102 : Growth Rate'

Note that all length measurements are given in pixels.