Phaedra, a Protocol-Driven System for Analysis and Validation of High-Content Imaging and Flow Cytometry

Abstract

High-content screening has brought new dimensions to cellular assays by generating rich data sets that characterize cell populations in great detail and detect subtle phenotypes. To derive relevant, reliable conclusions from these complex data, it is crucial to have informatics tools supporting quality control, data reduction, and data mining. These tools must reconcile the complexity of advanced analysis methods with the user-friendliness demanded by the user community. After review of existing applications, we realized the possibility of adding innovative new analysis options. Phaedra was developed to support workflows for drug screening and target discovery, interact with several laboratory information management systems, and process data generated by a range of techniques including high-content imaging, multicolor flow cytometry, and traditional high-throughput screening assays. The application is modular and flexible, with an interface that can be tuned to specific user roles. It offers user-friendly data visualization and reduction tools for HCS but also integrates Matlab for custom image analysis and the Konstanz Information Miner (KNIME) framework for data mining. Phaedra features efficient JPEG2000 compression and full drill-down functionality from dose-response curves down to individual cells, with exclusion and annotation options, cell classification, statistical quality controls, and reporting.

Molecular mechanism of respiratory syncytial virus fusion inhibitors

“…For each cell the mean GFP signal in the whole cell was computed and the single-cell data exported as text files. To calculate the percentage of infected cells per well, the single-cell measurements together with the original images and the segmentation masks of the cells and nuclei were imported to Phaedra 50 . After visual verification of the segmentation quality, a Knime workflow to classify each cell as infected or non-infected was executed.…”

SLAS Europe High-Content Screening Conference in Dresden: A Glimpse of the Future?

“…Janssen Pharmaceuticals developed its own image analysis solution (phaedra), and Novartis uses opensource software such as CellProfiler and KNIME. 15 Thus, different companies have come up with different solutions to address the issue of analyzing large data sets on computer clusters, whether in the cloud or on in-house computer farms.…”

Translation of a Tumor Microenvironment Mimicking 3D Tumor Growth Co-culture Assay Platform to High-Content Screening

“…20 The homogeneous proliferation assay using the alamarBlue reagent performed very well for the described 3D tumor growth assay, and if tumor mass is the only parameter of interest, it could be well used for primary screening, as data generation, handling, and analysis are much simpler and more convenient, particularly when screening of larger libraries is considered. However, we have developed a versatile and robust platform applying automated microscopy and image analysis that currently extracts already more parameters than a homogeneous assay could provide.…”

“…20 More than 50 cooperating views are available. An arbitrary number of views can be assembled within a so-called perspective (see Fig.…”