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>>colonyzer -h
Colonyzer 1.1.22.Unknown
usage: colonyzer [-h] [-c] [-m] [-p] [-i] [-x] [-q] [-r] [-e] [-k]
                 [-s SLOPEFILL] [-g] [-d DIR] [-l LOGSDIR] [-f FIXTHRESH]
                 [-u USEDICT] [-o FMT [FMT ...]] [-t UPDATES]

Analyse timeseries of QFA images: locate cultures on plate, segment image into
agar and cells, apply lighting correction, write report including cell density
estimates for each location in each image. If you need to specify initial
guesses for colony locations, you must provide a Colonyzer.txt file (as
generated by ColonyzerParametryzer) describing initial guess for culture array
in the directory containing the images to be analysed.

optional arguments:
  -h, --help            show this help message and exit
  -c, --lc              Enable lighting correction?
  -m, --diffims         If lighting correction switched on, attempt to correct
                        for lighting differences between images in timecourse
                        (can induce slight negative cell density estimates).
  -p, --plots           Plot spot location traces?
  -i, --initpos         Use intial guess for culture positions from
                        Colonyzer.txt file?
  -x, --cut             Cut culture signal from first image to make pseudo-
                        empty plate?
  -q, --quiet           Suppress messages printed to screen during analysis?
  -r, --remove          Remove Colonyzer output files from directory before
  -e, --endpoint        Only analyse final image in series. Mostly for testing
                        single image analysis.
  -k, --edgemask        During lighting correction, use intensity gradient &
                        morphology for final image segmentation instead of
  -s SLOPEFILL, --slopefill SLOPEFILL
                        Magnitude of slope defining edge of colony area.
                        Affects construction of pseudo-empty plate during
                        lighting correction as well as Trimmed & Area
                        measures. Default = 0.9
  -g, --greenlab        Check for presence of GreenLab lids on plates.
  -d DIR, --dir DIR     Directory in which to search for image files that have
                        not been analysed (current directory by default).
  -l LOGSDIR, --logsdir LOGSDIR
                        Directory in which to search for JSON files listing
                        images for analyis (e.g. LOGS3, root of HTS
                        filestore). Only used when intending to specify images
                        for analysis in .json file (see -u).
  -f FIXTHRESH, --fixthresh FIXTHRESH
                        Image segmentation threshold value (default is
                        automatic thresholding).
  -u USEDICT, --usedict USEDICT
                        Load .json file specifying images to analyse. If
                        argument has a .json extension, treat as filename.
                        Otherwise assume argument is a HTS-style screen ID and
                        return path to appropriate .json file from directory
                        structure. See in HTSauto package.
  -o FMT [FMT ...], --fmt FMT [FMT ...]
                        Specify rectangular grid format, either using integer
                        shorthand (e.g. -o 96, -o 384, -o 768 -o 1536) or
                        explicitly specify number of rows followed by number
                        of columns (e.g.: -o 24 16 or -o 24x16).
  -t UPDATES, --updates UPDATES
                        Number of (quasi-)randomly distributed grid positions
                        to assess in first phase of grid location. Ignored
                        when -initpos specified. Default = 144