## Sample parameters.txt file.
## Any line beginning with a # sign is ignored
## (do not, however, put pound signs in the middle of a line)

## Cell splitting parameters. If the cells perimeter divided the minimum
## distance between any two point of the cell boundary (waist) is more 
## than max_dist_over_waist then Cell ID will try splitting them. The split 
## will be done only if the waist (of the original cell) divided the minor
## axe of both new cells is less than max_split_over_minor. 
 max_split_over_minor 0.5
 max_dist_over_waist 8

## If you want to set different values for the first time point use
# max_split_over_minor_t0 0.5
# max_dist_over_waist_t0 8
 
 max_pixels_per_cell 3000
 min_pixels_per_cell 70

## The code makes an initial decision about the graylevels of the
## boundary pixels. To do this it takes the mean position of all the
## graylevels in the images and subtracts Z standard deviations. It then
## starts by considering all gray levels below this value as being
## parts of the cell borders. This value Z is the parameter
## background_reject_factor. Brightfield images taken slightly out of
## focus may do better with higher values (ie, higher values will
## better avoid spurious cells), but if the cell boundaries in the image
## are too narrow, a smaller value may be necessary--which might increase
## the level of background.
 background_reject_factor 1

## To track cells over time the program overlaps the pixel corresponding 
## to a given cell in the new time point with the found cells in the 
## previous time point. If the overlapping is higher than 
## tracking_comparison, the program assigns the same ID the cells in both
## time points.
# tracking_comparison 0.2


## To find the cell nucleus the program maximizes the fluorescence in
## a disc within the cell boundary. The radius in pixels of this disc 
## is specified by nucleus_radius_1. Cell-ID quantifies the fluorecence
## in concentric disc, which radius are defined by nucleus_radius_1 to
## nucleus_radius_6 (integer value in px units)
# nucleus_radius_1 2
# nucleus_radius_2 4
# nucleus_radius_3 5
# nucleus_radius_4 6
# nucleus_radius_5 7
# nucleus_radius_6 8


## Calculate all the fluorescence images variables on the bright field
## image as if it were a fluorescence image. This is potentially a good
## idea since it allows a good way to reject spurious cells. For example,
## the average value of the boundary pixels in good cells will be lower
## than the background level, but not so for spurious cells, etc.
## (Do not use when mapping by list order.)
# treat_brightfield_as_fluorescence_also


## Image type of the image that is used to find the cells
## Options are brightfield(default), metamorph_decon, hex_array
## or confocal_transmission
# image_type brightfield


## V1.2a Mapping of the fluorescence and bright field image can be based on 
## nearest times ("time" option) or  on the input lists, in which case both 
## list should have the same number of elements ("list" option). 
## Only use when file_type bf_fl_list is selected and 
## don't use treat_brightfield_as_fluorescence_also .
# bf_fl_mapping time
 bf_fl_mapping list

## If we have a "fret" image or not (a "fret" image here means that
## the image is split into an upper and lower half, each with its own
## excitation filter in front of it).
## The three arguments (bf_top_only, bf_bottom_only, bf_bottom_and_top)
## indicate where in the bright field image to look for the cells--since
## it's assumed that the bright field image also had its output sent
## throught the two excitation filters.
# fret bf_top_only
# fret bf_bottom_only
# fret bf_bottom_and_top

## More for the fret images. One of the fluorescence images will be
## used to identify the nucleus. Should it be the top or bottom image.
# fret nuclear_top
# fret nuclear_bottom

## If there is a third image type included, then this describes how
## to use it (nuclear_label means its a fluorescence tagged nucleus
## channel, vacuole_label means vacuole label)
# third_image vacuole_label
# third_image nuclear_label

##V1.2a TODO expand description
## Asumes nucleous in geometrical center of cell. Otherwise uses fluorescent 
## image to find nucleous. 
# force_nucleus_in_center

# output_individual_cells

## "do_recombination" to try to connect cells using cuts on fluorescence
## "recombination_fl_per_a_nucleus F CUT" is cut below which we consider the
## cell has no nucleus. "F" is the "flag" given to the fluorescence type we're
## going to use for the cut.
## "recombination_is_a_cell_fl_per_a F CUT" is minimum fluorescence/area to
## consider the cell a real cell (a way to get rid of junk). This is only
## used for recombining cells. Ie, for recombining cells we only consider
## cells above CUT but we don't throw away those that fail. "F" is the flag
## for the fluorescence type to use.
## "recombination_all_new_cells": All cells produced after i_t 0 will be 
## recombined.
# do_recombination
# recombination_fl_per_a_nucleus 1 2500.0
# recombination_is_a_cell_fl_per_a 3 500.0
# recombination_all_new_cells

## allow wiggling between the brightfield and fluorescence images
 align_individual_cells

## if you want to wiggle within a boundary use 
## align_individual_cells_boundary insted of align_individual_cells

##Cell ID allows to correct for bad repositioning of the field between frames
##adding an offset to when required.
##If we want to use the first fluorescence image to align all the others
##then use the option align_fl_to_first
##If you want to align the fluorescent images to the bright field image use
##the align_fl_to_bf option


## append_output means that when we write out the output files
## we're going to _add_ to the end of the files instead of making
## new ones.
## the argument is the offset to add to the id numbers
# append_output 1000
