####################
# Basic properties #
####################

# If number of pixels of a cell on the first frame it appears on is bigger than this value
# the algorithm will ignore the cell by not trying to find its mother. 
# NOTE: 
# - keep this value low to ignore cells that changed ID during lifetime because of Cell ID 
#   segmentation problems
# - keep this value reasonably higher than 'min_pixels_per_cell' parameter of Cell ID  
# Original value: 	400 (because in some cases we used 'min_pixels_per_cell' = 250)
# Suggested range:	300-400 (300 for values of 'min_pixels_per_cell' lower than 150)
max-new-born-cell-pixels = 400 

# If number of pixels of a cell one frame before another cell appeared on is smaller than this value
# the algorithm will not take the cell into account as the mother candidate of the new born cell.
# NOTE: 
# - original value for this property gave 100% of correct results on test data 
# - making this value reasonably higher than 'min_pixels_per_cell' should filter most cells that are
#   to young to be a parent out from parent candidates 
# - it makes sense to keep this value lower than 'max-new-born-cell-pixels' if the latter is higher
#   than 300
# Original value: 	300
min-parent-pixels = 300

# Parent needs to exist on one at least one of 'max-parent-shift' frames before child appears.
# NOTE:
# - increase the value if segmentation quality is poor and parent cell may not be recognized on 
#   the frame that is directly before the frame that the child appeared on 
# - if segmentation quality is perfect this value should be equal to 1 (the lowest correct value)
# Original value: 2 
# Suggested range: 1-3
max-parent-shift = 2

# Minimal number of frames on which a real cell should have stable nucleus area (a.nucl = 49.0).
# Otherwise the algorithm will ignore the cell marking it as a fake cell.
# Original value:		3
# Suggested range:	2-3
min-stable-nucleus-area-frames = 3

# The shape of a new born cell should not be too far from a circle. Eccentricity of a cell
# is its min.axis/maj.axis ratio and its value should in range of (0,1] where 1 means that
# cells shape is very close to circle. 
# If eccentricity of a cell on the first frame it appears on is lower than this value 
# the algorithm will ignore the cell marking it as a fake cell.
# NOTE:
# - using eccentricity for 'fake' cell detection is less reliable than using nucleus size 
#   (see 'min-stable-nucleus-area-frames' property description above)
# - to ignore cell eccentricity set the value to 0 as every cell will have bigger eccentricity
# Original value: 	0.5
# Suggested range: 	0-0.5
min-new-born-cell-eccentricity = 0.5

# The algorithm will try to find mother of a new appearing cell only if it appeared later than 
# 'number-of-first-frames-to-ignore' and earlier than 'number-of-first-frames-to-ignore' frames 
# before the end of the movie.
# NOTE:
# - if a cell appears at the beginning/end of the movie it is very unlikely that the algorithm has 
#   enough data to correctly find its mother
# - it is difficult for the algorithm to distinguish fake cells from real cells	if they appear near
#   the end of the movie
# Original value:		5 (both properties)
number-of-first-frames-to-ignore = 5
number-of-last-frames-to-ignore = 5

# When cells fluorescence mean gets above this value it is a clear indication that the cell is dying.
# From that moment (frame) the cell will not be taken into account as a parent candidate.
# Original value: 	3000
# Suggested range: 	2500-3000
max-f-mean-of-living-cell = 3000

# If there are more parent candidates after parent filtering phase of algorithm the new born cell 
# will be ignored by the algorithm by not trying to choose its mother. 
# NOTE: 
# - keep this value low for most reliable results 
#   (increasing the value decreases false negative rate but increases false positive rate)
# Original value: 	1
# Suggested range: 	1-2
max-parent-candidates = 1

# Frame window radius used to check if there are any other frames close that also hold information
# about the cell. If not then the cell on the frame is considered fake and the frame data will be 
# removed from the output.
# Radius of X means that the cell that existed on a cell on frame N should also exist on one of 
# the frames in ranges: [N-X, N-1], [N+1, N+X]. If X is less then 1 this fake frame detection is
# disabled. 
# NOTE:
# - it doesn't ignore all frames of a cell with a certain id like other fake detection filters
# - it helps to remove fake cells that existed on frames at the beginning of movie but preserve 
#   frames of a real cell that got the same id as the fake cell later in the movie
# Original value:		2
# Suggested range:	0-2
isolated-fake-frame-removal-window = 2

########################################################
# Properties used for filtering best parent candidates #
########################################################

# Should additional debug information about filter computations be in the output. 
# Original value: true
debug-enabled = true

# Frame window radius used to calculate smooth fluorescence deviation values (to ignore noise)
# which will be used in computations for filtering best parent candidates.
# Radius of X means that f.deviation.smooth of a cell on frame N is the average of f.deviation
# of the cell on frames in range [N-X, N+X].  
# Original value:		5
smooth-f-deviation-window = 5

# Mother should have very similar fluorescence as daughter in first few frames after the daughter
# appeared. The next few properties are used to specify required fluorescence similarity degree for 
# parent candidate of a new born cell to be considered a better candidate:
#
# Whether this filter should be used by algorithm at all (true/false).
# Original value: 	true
beginning-f-window-filter-enabled = true
 
# Length of a window of consecutive frames to be used in comparison  
# Original value: 	5
beginning-f-window-length = 5
# Maximal offset between first frames of mother and daughter windows to be used in comparison
# NOTE: 
# - it should rather be very low not to reduce algorithm reliability and performance
# Original value: 	2 
beginning-f-window-max-offset = 2
# Maximal number of missing candidate or daughter frames in compared windows
# NOTE: 
# - it should rather be very low not to reduce algorithm reliability
# Original value: 	2 
beginning-f-window-max-missing = 2
# Maximal average difference between fluorescence values of mother and daughter in corresponding
# frames of their windows. 
# Original value: 	50.0
beginning-f-window-max-avg-diff = 50.0

# Mother should have a fluorescence peak raise (short: peak) in the same point of time as first 
# peak of the daughter. The next few properties are used to specify peaks and their similarity. 
#
# Whether this filter should be used by algorithm at all (true/false).
# Original value: 	true
first-peak-filter-enabled = true
# Maximal frame distance between the frame that the child appeared on and the beginning of its peak
# Original value:		50
first-peak-max-child-offset = 50
# Maximal frame distance between starting points of daughter and mother peaks.
# Original value:		10
first-peak-max-parent-offset = 10 
# Maximal number of missing candidate or daughter frames in their peaks
# NOTE: 
# - it should rather be very low not to reduce algorithm reliability
# Original value: 	2 
first-peak-max-missing = 2
# Minimal number of frames with a fluorescence raise to consider it a peak.
# Original value:		3
first-peak-min-length = 3
# Minimal raise between fluorescence values of two consecutive frames to consider it part of a peak.
# Original value:		5.0
first-peak-min-frame-height-diff = 5.0
# Maximal number of exceptions from the rule using 'first-peak-min-frame-height-diff' (number of
# drops/raises lower than 'first-peak-min-frame-height-diff' allowed between consecutive frames)
# NOTE: 
# - it should rather be very low not to reduce algorithm reliability
# Original value:		2
first-peak-max-frame-height-diff-exceptions = 2
# Minimal total difference of fluorescence values in a time fragment to consider it a peak.
# Original value:		100.0
first-peak-min-total-height-diff = 100.0