The cell data files
For each cell a separate .mat file is created with a separate id under the xy#/cell/ directory. Files starting with a capital letter ‘C’ went through a full cell cycle (birth and death/division), where as a small ‘c’ indicates a non full cell cycle. A short tutorial on sample analysis using the cell files can be found here.
Each single-cell file has the following information:
- CellA: a cell array with frame-by-frame information (details below)
- death: frame at which the cell divided or disappeared
- birth: frame at which the cell was born or appeared
- divide: 1 if successful division was observed
- sisterID: id of the sister cell
- motherID: id of the mother cell
- daughterID: ids of the two daughter cells
- ID: id of the cell
- neighbors: ids of the cells neighboring this cell
- stat0: 0: birth was not observed, 1: division was not observed, 2: Full cell cycle
- ehist: history of errors, sum of all errors
- contactHist: number of neighboring cells
There is one CellA structure for each frame during the lifetime of the cell. The frame_number starts from one, and goes up to cell's lifetime. Here is an example for of the data.CellA structure
data.CellA{frame_number} =
- xx: coordinates of padded bounding box in x -axis
- yy: coordinates padded bounding box in y -axis
- mask: logical (1 and 0) image of the cell mask, unoriented
- r_offset : global coordinates of the top left edge of the cell’s bounding box, useful for plotting quantities at global coordinates on the mask, phase and fluor with the size of the bounding box.
- BB: start and end coordinates of padded cell bounding box
- edgeFlag: true if the cell is at the edge of the image
- phase: the cropped phase image of the cell
- coord: coordinates, area, and orientation, see below
- length: (1) length and (2) width of the box surrounding mask
- cellLength: (1) max length and (2) mean width of the cell
- pole : orientation of the cell pole, see below
- fluor1 : image for the first fluorescence channel (fluor2 if there is a 2nd channel)
- fuor1mm : min and max of fluorescence channel 1 (fluor2mm if there is a 2nd channel)
- fl1 : statistics of fluor1, see below (fl2 if there is a 2nd channel)
- cell_dist : distance to the edge of the colony
- gray : average phase gray value in cell region
- locus1 : Focus fitting for channel 1, see below (locus2 if there is a second channel)
- r : global coordinates of cell centroid (midpoint of cell)
- error: segmentation error list
- ehist : ehist is the sum of all errors in the region’s history
- contactHist : 1 if cell is in contact with other cell
- stat0: 0 if cell birth was not observed, 1 if cell birth was observed but no good division at the end of the lifetime, 2 if good cell birth and division were observed.
The coord field contains a lot of cell specific information related to cell coordinates:
data.CellA{frame_number}.coord =
- A: Area of cell mask
- r_center: geometrical center of the cell (global coordinates)
- box: coordinates of box surrounding cell (along e1 and e2 with length and width of the cell)
- xaxis: coordinates of major principal axis (end and start point)
- yaxis: coordinates of minor principal axis (end and start point)
- I: Moment of inertia of cell mask
- e1: major principal axis unit vector
- e2: minor principal axis unit vector
- rcm: position of center of mass for the cell mask (global coordinates)
The pole field contains info pertaining to the cell pole and pole ages:
data.CellA{frame_number}.pole =
- e1: major principal axis unit vector
- op_ori: 1 if old pole is in the direction of e1, -1 if the old pole is in the opposite direction.
- op_age: age of old pole in cell cycles, NaN if no birth is observed
- np_age: age of new pole in cell cycles
The locus field contains information from foci fitting:
data.CellA{frame_number}.locus1(foci_number) =
- r: locus position (global coordinates)
- score: score of how good of a focus it is. It combines intensity and foci fitting (Intensity * fitScore / (sqrt(pi) * fitSigma))
- intensity: raw maximum intensity of the focus
- normIntensity: same as raw intensity above...
- fitSigma: standard deviation (spread) of gaussian fit to the focus.
- fitScore: score of Gaussian fit to the focus. A measure of the overlap of the two distributions, the focus and the gaussian fit.
- shortaxis: focus position along the cell’s short axis in local coordinates (0 is the cell center)
- longaxis: focus position along the cell’s long axis in local coordinates (0 is the cell center)
The fluor field contains statistics about cell fluorescence. fl1 is the first fluorescence channel (c2 images), fl2 the second fluorescence channel etc.
data.CellA{frame_number}.fl1 =
- sum : sum of fluorescence
- r : the coordinates of the center of mass of the fluorescence
- Ixx : 2nd moment of fluorescence along X
- Iyy : 2nd moment of fluorescence along X
- Ixy : 2nd moment of fluorescence along XY