Frame files

The _seg.mat data files

A seg file is created for each time frame and in each xy position, during the first pass of segmentation. It contains the following information :

• mask_bg: image of background mask, where cell clumps are white (1) and background is black (0)
• mask_cell: image where the cells appear white and the background is black
• phase: original phase image
• crop_box: alignment information for the specific image
• segs: structure explained below
• phaseMagic: phase image with magicContrast applied to increase subcellular contrast
• segs_good: image with the segments determined as correct
• segs_bad: image with the segments determined as incorrect
• segs_3n: image with the segments determined as should never be switched off
• segs_label: image of bwlabel of good and bad segs.
• score: array of scores for each segment
• scoreRaw: array of raw score for each segment
• props: array of properties for each segment
• info: array of segment parameters that are used to generate the raw score, look below

1. the minimum phase intensity on the seg
2. the mean phase intensity on the seg
3. area of the segment
4. the mean second d of the phase normal to the seg
5. second derivative of the phase normal to the seg at the min pixel
6. second derivative of the phase parallel to the seg at the min pixel
7. min area of neighboring regions
8. max area of neighboring regions
9. min lengths of the minor axis of the neighboring regions
10. max lengths of the minor axis of the neighboring regions
11. min lengths of the major axis of the neighboring regions
12. max lengths of the major axis of the neighboring regions
13. length of minor axis of the segment
14. length of major axis of the segment
15. square of length of major axis
16. max length of region projected onto the major axis segment
17. min length of region projected onto the major axis segment
18. max length of region projected onto the minor axis segment
19. min length of region projected onto the minor axis segment

The _err.mat data files

There is also an err file for each time frame and in each xy position. The err file is created after the linking and error resolution phase of segmentation. They contain the same information as the _seg.mat files above with one extra structure called regs :

• regs: [1x1 struct]
  • regs_label: an image with pixels of 0 where the background is, and pixels of the id of the region located there.
  • props:structure of properties generated by regionprops
  • num_regs: number of regions found
  • dA: area change for the linking in the map from r
  • eccentricity: array of long axis of region / short axis of region
  • L1: array of long axis length of each region
  • L2: array of short axis length of each region
  • contact: array, 1 if region is in contact with another region (<5 pixels)
  • neighbors: cell array of IDs of neighbors of each region
  • contactHist: array, 1 if cell has been in contact with other cells
  • scoreRaw: region’s raw score
  • death: array with frame of region death/division
  • deathF: array with 1 if region died, divided in this frame
  • birth: array with frame of cell birth
  • birthF: array, true if region was born in this frame
  • age: array for region’s age in frames
  • divide: array, 1 if division was observed
  • ehist: array with sum of errors up to this frame in cell history
  • stat0: array with cell status, 0 - error or birth not observed, 1 - cell was the result of a good birth, 2 - cell was result of good birth and divided successfully (set by trackOptiCellMarker)
  • sisterID: array with Cell ID of sister cells/regions
  • motherID: array with Cell ID of mother cell/region
  • daughterID: cell array with Cell ID of daughter cells
  • ID: ID of each cell
  • map: map structure
  • error: error structure with the following fields
    • .f: error found from current -> forward frame
    • .r: error found from current -> reverse frame
    • .label: String containing a description of the error
  • info: the fields used for scoring the regions. The fields can vary according to the scoring function used in CONST.regionScoreFun.fun. The names of the fields should be at CONST.regionScoreFun.names.

For cellprops3 the fields in info are the following :

1. long axis of the region
2. mean of the short axis of the region
3. neck width
4. maximum of the short axis of the region
5. variance of the short axis of the region
6. mean of width sin pi s/S
7. mean of width sin pi 2s/S
8. mean of width sin pi 3s/S
9. RoundIndOver
10. RoundIndUnder
11. Area
12. max dtheta^2
13. mean of theta sin pi s/2S
14. mean of theta sin pi s/S
15. mean of theta sin pi 3s/2S
16. mean of theta sin pi 2s/S
17. 1/long axis
18. 1/mean short axis
19. Min End Width
20. round end min
21. round end max