WP13.1 Strategic Review of Cell Phenotype Image (CPI) Data Resource

1. WP13.1Strategic Review of Cell Phenotype Image (CPI) Data Resource Wolfgang Huber EMBL-EBI

2. Cell-based, high-throughput screens using mscopy will be a major innovative force in the biology of the next decade in specialized laboratories for several years, but now entering mainstream due to developments in availability of screening reagents; automation of assays, robotics, data analysis; live-cell imaging versatile tool for wide range of areas in cell biology, developmental biology and genetics 17./18. 7. 2008: workshop hosted by EBI at WT conf centre in Hinxton

3. An example: genome-wide morphology screen Genome-wide RNAi library (Dharmacon, ~22000 genes) HeLa cells, incubated for 48h, then fixed and labeled Microscopy readout: DNA (DAPI),Tubulin (Alexa), Actin (TRITC) Data: ca. 90,000 images (170GB) Collaboration between Boutros department (DKFZ) and Huber group (EBI) wt- wt- wt- BTDBD3 CEP164 CD3EAP

4. Prototype web-database Initially for our own browsing of the data Now for the publication of the data

5. Prototype web-database • Allows download of • original full-resolution TIFF files • compressed visualisation summaries at various stages • the Bioconductor analysis software

6. Workshop participants Organisers: W. Huber, E. Birney (both EBI), M. Boutros (DKFZ), J. Ellenberg (EMBL HD) Rebecca Aarons (WT) Midori Harris (EBI) Michael Howell (CRUK) Karol Kozak (ETHZ) Emma Lundberg (KTH) Fernand Meyer (ENSMP) Carmel Nanthakumar (GSK) Wiro Niessen (ErasmusMC) JC Olivo-Marin (Paster) Jeroen Raes (EMBL) Mihail Sarov (MPI-CBG) Jason Swedlow (Dundee) Stefan Wiemann (DKFZ) Thomas Baer (OSA) Buzz Baum (UCL) Andy Blanchard (GSK) Alvis Brazma (EBI) Stephen Bryant (NCBI) Anne Carpenter (MIT) Daniel Gerlich (ETHZ) Jean Karim Heriché (EMBL) Andy Lyall (EBI) Erik Meijering (ErasmusMC) James Mulshine (OSA) Lucas Pelkmans (ETHZ) Rainer Pepperkok (EMBL) Jasmine Zhou (USC)

7. Three areas of coordination and collaboration To avoid duplication and make the field advance faster Analysis tools: software algorithms for image analysis (segmentation, feature extraction in high-throughput settings), visualisations for quality assessment, data analysis Training: knowledge how to scale up assays for automation; robotics; use and further advance of image and data analysis algorithms Dataset sharing and aggregation: providing datasets to the public; bringing datasets from different sources together to create more comprehensive views of biological systems.

8. Community dynamics We can learn from previous experience. Genome projects: conducted in specialized, technologically advanced sequencing centres. Immediate data publication (Fort Lauderdale). Public access through portals such as Ensembl or UCSC. Microarrays: application of the technology is distributed across many academic institutions and companies, much more chaotic landscape of datasets. MGED, MIAME: data reporting standards; publication concurrent with publication of scholarly article. Due to the diversity of biological questions, specialized expertise needed to set up assays, comparatively modest cost, and the versatility of a screening microscope, CPI will be more analogous to microarrays than to centre-based genome projects.

9. Pilot database will be set up by EBI, in close collaboration with the community EBI will explore the suitability of the software platform currently powering Mitocheck database (J.K. Heriché and co-workers). Is currently already being used at EMBL-HD to aggregate results from 3 different screens. Initially, scope limited to human cell lines treated with genome-wide RNAi libraries. These groups have expressed their interest in contributing datasets: Ellenberg, Heriché (Mitocheck) Pepperkok (Secretion) Boutros, Huber (Morphology) Pelkmans Gerlich Carpenter