Protocols generated by the Systems Microscopy NoE, or links to such protocols, will be found here as the project progresses.
http://www.bioconductor.org/packages/release/data/experiment/vignettes/HD2013SGI/inst/doc/HD2013SGI.pdf provides a detailed, step-by-step description of the analysis of a systems microscopy experiment including the image analysis, cell segmentation, feature extraction, statistical analysis. In addition, a downstream biological application is performed, in this case, to combinatorial RNAi screening on human cancer cells. The landing page for the associated software package is here: http://www.bioconductor.org/packages/release/data/experiment/html/HD2013SGI.html
A more specialised protocol, for the analysis of tandem fluorescent timers in the paper doi:10.1038/nature12635 is provided by http://www.bioconductor.org/packages/devel/data/experiment/vignettes/DonaPLLP2013/inst/doc/PLLPanalysis.pdf