parameters_description.txt

## Sample parameters.txt file.
## Any line beginning with a # sign is ignored
## (do not, however, put pound signs in the middle of a line)
 max_split_over_minor 0.5
 max_dist_over_waist 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 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 1.5


## 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.
# treat_brightfield_as_fluorescence_also


## Image type of the image that is used to find the cells
image_type brightfield

## 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


## "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.
# do_recombination
# recombination_fl_per_a_nucleus 1 2500.0
# recombination_is_a_cell_fl_per_a 3 500.0

## allow wiggling between the brightfield and fluorescence images
 align_individual_cells


# 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