It sounds like you want to run CellProfiler ‘headless’:
% *** RUNNING CELLPROFILER WITHOUT THE GRAPHICAL USER INTERFACE ***
% In order to run CellProfiler modules without the GUI you must have the
% following variables:
% handles.Settings.ModuleNames (for all modules in pipeline)
% handles.Settings.VariableValues (for all modules in pipeline)
% handles.Current.CurrentModuleNumber (must be consistent with pipeline)
% handles.Current.SetBeingAnalyzed (must be consistent with pipeline)
% handles.Current.FigureNumberForModuleXX (for all modules in pipeline)
% handles.Current.NumberOfImageSets (set by LoadImages, so if it is run
% first, you do not need to set it)
% handles.Preferences.IntensityColorMap (only used for display purposes)
% handles.Preferences.LabelColorMap (only used for display purposes)
% handles.Preferences.FontSize (only used for display purposes)
% You will also need to have the CPsubfunctions folder, since our Modules
% call CP subfunctions for many tasks. The CurrentModuleNumber needs to be
% set correctly for each module in the pipeline since this is how the
% variable values are called. In order to see what all of these variables
% look like, run a sample analysis and then go to File -> Tech Diagnosis.
% This will let you manipulate the handles variable in MatLab.
So yes, you are correct- you will need to set some parameters. This option requires you have a Matlab license on the linux machine that you’ll be using for analysis. You’ll launch matlab interactively, set up the handles, and run the pipeline from the Matlab command line.