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News 2020-10-12

EOSC-Life Collaboration Integrates CellProfiler into Galaxy


Scientists now have a comprehensive suite to perform tasks in image analysis workflows that can be run in the cloud.

European Research Infrastructures Euro-BioImaging and ELIXIR, in collaboration with the Image Data Resource (IDR) and Galaxy Europe, have have integrated CellProfiler, an image analysis software with a focus on recognizing cellular components, into Galaxy, a key cloud workflow tool, in order to facilitate the use and re-analysis of publicly available datasets. These developments are a major step forward for life scientists, who can now run image analysis algorithms on large openly available image datasets to address different biological questions in the cloud.

In total, Euro-BioImaging and ELIXIR integrated 22 CellProfiler modules into 19 Galaxy tools, providing scientists with a comprehensive suite to perform tasks such as object segmentation and feature extraction in image analysis workflows that can be run in the cloud.

Scientists can upload their own images to a Galaxy instance and build workflows combining these tools to address different biological questions.

In addition, scientists may use these workflow tools to gain new insights by re-analysing previously published publicly available datasets, such as those arising from large-scale screening efforts. To facilitate the reuse of such public datasets from the Image Data Resource (IDR), a Galaxy tool to make bulk-downloads possible was developed in collaboration with the European Galaxy team partners in EOSC-Life.

The European Open Science Cloud (EOSC) is a digital platform for the European science community, designed to give researchers from the European Union (EU) a global lead in research data management. Within this overarching project, EOSC-Life brings together the 13 Life Science Research Infrastructures (LS RIs) to create an open, digital and collaborative space for biological and medical research.

 

Read more about this EOSC-Life success story here:

https://www.eurobioimaging.eu/news/euro-bioimaging-contributes-to-cloud-based-biological-image-analysis-workflow-tools-/

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