R/Bioconductor package that provides general purpose functionality for the reading, writing, processing and analysis of images. In the context of high-throughput microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors.

Homepage

http://bioconductor.org/packages/release/bioc/html/EBImage.html

Contact

Mike Smith

Workflows and tools for analysis of microscopy image data and cellular phenotyping using Galaxy. Provision of expertise and support of projects requiring automatic image analysis.

Homepage

https://github.com/BMCV/galaxy-image-analysis

Contact

PD Dr. Karl Rohr
Thomas Wollmann

GenomeCRISPR is a database for high-throughput screening experiments performed by using the CRISPR/Cas9 system. A dynamic web interface guides users through the process of finding information about published CRISPR screens. The database holds detailed data about observed hits and phenotypes. Moreover, it provides knowledge about performance of individual single guide RNAs (sgRNAs) used under various experimental conditions.

Homepage

http://genomecrispr.dkfz.de

Relevant Publications

Rauscher B, Heigwer F, Breinig M, Winter J, Boutros M. GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens. Nucleic Acids Res. 2017;45(D1):D679-D686.

Contact

Michael Boutros (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Ulrike Hardeland (This email address is being protected from spambots. You need JavaScript enabled to view it.)

The GenomeRNAi database makes available RNAi phenotype data extracted from the literature, or submitted by data producers directly, for human and Drosophila. It also provides RNAi reagent information, along with an assessment as to their efficiency and specificity.

Homepage

http://www.genomernai.org/

Relevant Publications

Schmidt EE, Pelz O, Buhlmann S, Kerr G, Horn T, Boutros M. GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Res. 2013;41(Database issue):D1021-6.

Contact

Michael Boutros (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Ulrike Hardeland (This email address is being protected from spambots. You need JavaScript enabled to view it.)

This KNIME framework is a data mining platform including manifold libraries for image processing (based on Fiji/ImageJ) and data exploration. The platform provides access to workflows and pipelines for (large-scale) automated phenotype analysis.

Contact

Holger Erfle (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Dr. Manuel Gunkel

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