The Source_Directory can be either an ‘R_’ directory to run both the image processing and signal processing steps on the data set, or a ‘D_’ directory to run only the signal processing step. If a run (‘R_’) directory is specified, the *.png (or legacy *.pif) files must be present in the rawImages subdirectory of the Run directory. If a data (‘D_’) directory is specified, the directory must contain image processed results. If the data present in a ‘D_’ directory has also been signal processed, the runAnalysisPipe command will produce a warning message (note that this is only a warning; processing will still proceed).
