Euro-BioImaging contributes to cloud-based biological image analysis workflow tools

September 2, 2020
Image Analysis Data analysis EOSC

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. Project partners Euro-BioImaging and ELIXIR, in collaboration with the Image Data Resource (IDR) and Galaxy, have contributed to one of EOSC-Life’s earliest success stories, by bringing important image analysis tools to the cloud.  

Introducing important functionalities to the cloud

Euro-BioImaging and ELIXIR, in collaboration with the Image Data Resource (IDR) and Galaxy Europe, have facilitated the use and re-analysis of publicly available datasets by integrating CellProfiler, an image analysis software with a focus on recognizing cellular components, into Galaxy, a key cloud workflow tool. These developments are a major step forward for biologists, who will be able to run image analysis algorithms on large openly available image datasets to address different biological questions in the cloud. 

In total, Euro-BioImaging and ELIXIR have worked together to integrate 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.

Benefiting from shared data repositories

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

Providing exemplary workflows & training

An exemplary workflow has been created using these tools as part of a Demonstrator project of EOSC-Life. This workflow, which focuses on reusing datasets from publicly available RNAi screens to investigate the nucleoli, is available at the registry Workflow Hub.

To ensure these developments are accessible to all, a GTN tutorial was created reproducing the work done in this project.

An important contribution to data-driven life science research

The integration of CellProfiler modules into Galaxy allows biologists to manipulate large image datasets – including shared datasets – in cloud workflows, performing semi-automated imaging analysis for faster results. This is an important step for the biological research community, which will benefit from better access to shared data and faster image analysis. And it’s an important contribution towards the EOSC-Life mission of supporting management, storage and reuse of data in the cloud - for excellent data-driven life science research.

For more information about CellProfiler in Galaxy:

For more information about Euro-BioImaging’s contribution to EOSC-Life:

Euro-BioImaging is a strong partner in the EOSC-Life project, leading 2 major work packages. EOSC-Life started in March 2019, connects the 13 ESFRI research infrastructures in the Health and Food domain to create an open collaborative digital space for life science in the European Open Science Cloud. In EOSC-Life, the research infrastructures will publish data from facilities and data resources in the cloud and link these FAIR* databases to open and reusable tools and workflows accessible to users via Europe’s national and international life-science clouds. To achieve its objectives, EOSC-Life will run a series of Open Calls for user research which will allow Europe’s large research community to adopt advanced data management practice and access data integration and large-scale analysis tools in the cloud.

* FAIR data meet principles of findability, accessibility, interoperability, and reusability

Want to participate in future cloud developments?

As part of EOSC-Life, a series of Open Calls will be held to support research projects that adopt advanced data management practices or promote data integration and analysis tools in the cloud. To learn more about the current Open Calls, please visit the EOSC-Life website:

More news from Euro-BioImaging

July 12, 2024

Latest developments in cryo-EM and a goodbye to iNEXT-Discovery

The final consortium meeting of the iNEXT-Discovery project took place in Brno in June 2024, alongside the Symposium on Recent Advances in Cryo-EM. This…

July 10, 2024

Contribute to the "Inner Cosmos" art project

Inner Cosmos is an art project by Euro-BioImaging aimed at reaching the general public. The video has been designed as part of an installation…

Overview of the Node-to-Node exchanges from the 12 selected applications to the first round of the Job Shadowing program

July 10, 2024

Participants selected for the first Euro-BioImaging Cross-Node Job Shadowing program!

Open to all Euro-BioImaging Node Staff, the Cross-Node Job Shadowing program is a unique and exciting initiative implemented through…