For a more detail description of each parameter read parameters.txt

Example:
  cell -b Bright.txt -f Fluor.txt -p parameters.txt

  Bright.txt: A list of the brightfield images names
  Fluor.txt: A list of the fluorescence images names
  parameters.txt: See example file.

Usage:
  cell.exe [OPTION...] - Cell ID options

Help Options:
  -?, --help                     Show help options
  --help-all                     Show all help options
  --help-cell                    Parameters used to find cells
  --help-image-type              Specifications for the input images
  --help-misc                    Miscelaneus options

Application Options:
  -b, --bright                   Text file list of brightfield tif images
  -f, --fluor                    Text file of fluorescent tif images
  -3, --third                    List of third images to be used
  -d, --dark=dark.txt            List of dark images to be used
  -t, --flat=flat.txt            List of flat images to be used
  -p, --param=parameters.txt     Parameters file 
  -o, --output                   Basename of output files (including dirs)


>cell --help-all

*** Cell_ID Version 1.2a *** 

Usage:
  cell.exe [OPTION...] - Cell ID options

Help Options:
  -?, --help                     Show help options
  --help-all                     Show all help options
  --help-cell                    Parameters used to find cells
  --help-image-type              Specifications for the input images
  --help-misc                    Miscelaneus options

Cell Segmenting
  --brf                          background_reject_factor segmentation parameter
  --max-ppc                      max_pixels_per_cell segmentation parameter
  --min-ppc                      min_pixels_per_cell segmentation parameter
  --max-som                      max_split_over_minor cell splitting parameter
  --max-dow                      max_dist_over_waist cell splitting parameter
  --max-som-t0                   max_split_over_minor_t0 cell splitting parameter
  --max-dow-t0                   max_dist_over_waist_t0 cell splitting parameter
  --track                        tracking_comparison parameter
  --align-fl                     align_fl_to_first/bf option (first, bf)
  --nucl1			 nucleus_radius_1 parameter
  --nucl2			 nucleus_radius_2 parameter
  --nucl3			 nucleus_radius_3 parameter
  --nucl4			 nucleus_radius_4 parameter
  --nucl5			 nucleus_radius_5 parameter
  --nucl6			 nucleus_radius_6 parameter

Image Type options
  --fret-bf                      fret_bf options for split images (top, bottom or both)
  --fret-nuclear                 fret_nuclear options for split images (top, bottom )
  --image-type=bright            image_type options (bright, decon, hex, confocal)
  --3-img-label=none             third_image label option (nuclear, vacuole)

Miscelaneus options
  --force-nuc                    force_nucleus_in_center option
  --list-mapping                 bf_fl_mapping list
  --bf-as-fl                     treat_brightfield_as_fluorescence option
  --align-ind                    align_individual_cells option
  --align-ind-boundary           align_individual_cells_boundary option
  --output-ind                   output_individual_cells option
  --append_output                append_output option, argument is the id-offset (>=0)

Application Options:
  -b, --bright                   Text file list of brightfield tif images
  -f, --fluor                    Text file of fluorescent tif images
  -3, --third                    List of third images to be used
  -d, --dark=dark.txt            List of dark images to be used
  -t, --flat=flat.txt            List of flat images to be used
  -p, --param=parameters.txt     Parameters file 
  -o, --output                   Basename of output files (including dirs)

