Protocols generated by the Systems Microscopy NoE, or links to such protocols, will be found here as the project progresses.

“Multivariate Phenotyping” 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:

“A software framework for analysing and reporting high-throughput microscopy-based screens"

The imageHTS package for R provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopy-based datasets.

"Analysis of tandem fluorescent timers"

A more specialised protocol, for the analysis of tandem fluorescent timers in the paper doi:10.1038/nature12635 is provided by


Seventh Framework Programme

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