Running MoMA from the command line

In order to run MoMA from the command line, you need to follow the installation instructions here first: Installation guide

Afterwards, you can execute MoMA like this:

java -jar MotherMachine_-0.10.0.jar -i /absolute/path/to/input/folder/

Please note, that -i is a mandatory parameter followed by the input folder containing only a single growth channel splitted by the procedured introduced here: Growth Channel Separation

The -c option followed by the number of color channels is mandatory as well.

You get a full list of available command line options by entering the -help option:

$ java -jar MotherMachine_-0.10.0.jar -help

usage: ... [-p props-file] -i in-folder [-o out-folder] -c <num-channels>
           [-cmin start-channel-ids] [-tmin idx] [-tmax idx] [-orange
           num-frames] [-headless]
 -cmin,--min_channel <arg>   the smallest channel index (usually 0 or 1,
                             default is 1).
 -h,--headless               start without user interface (note:
                             input-folder must be given!)
 -help                       print this message
 -i,--infolder <arg>         folder to read data from
 -o,--outfolder <arg>        folder to write preprocessed data to (equals
                             infolder if not given)
 -orange,--opt_range <arg>   initial optimization range
 -p,--props <arg>            properties file to be loaded (mm.properties)
 -tmax,--max_time <arg>      last time-point to be processed
 -tmin,--min_time <arg>      first time-point to be processed