New resources for image analysis available in Galaxy


March 15, 2024
AI4Life Data analysis

Galaxy is a free, open-source cloud-based system for analyzing data, authoring workflows and much more. A number of tools and resources for the imaging community are available via Galaxy. To further develop these resources, an "Image Analysis in Galaxy" hackathon was held from February 26th to March 1st, 2024, at the University of Freiburg (Germany). Co-organized by Euro-BioImaging and NFDI4BIOIMAGE, the event aimed to enhance image analysis capabilities and workflows within the Galaxy platform.

Here are some of the main outcomes and how they can be useful to you:

  • Napari CellProfiler have now been integrated into Galaxy as interactive tools. This means that you can now use both applications in the same way as you’d do in your local workstation but with the computational capabilities of high-performance or cloud computing resources in the backend.
  • Cellpose is now available as a Galaxy tool. Cellpose is a deep learning-based segmentation tool widely used in the image analysis field. The integration of Cellpose into Galaxy harnesses the HPC resources, enabling users to perform segmentation tasks on a wide range of images with enhanced computing power.
  • Integration of BioImage Model Zoo: The AI4Life project hosts a repository of advanced AI models, the BioImage Model Zoo (BMZ). Models from the BMZ are now available via Galaxy as remote data and a general-purpose tool is being developed to make inferences on test images using Galaxy.
  • Visualisation: It’s now possible to explore TIFF files on Galaxy and work is being done so you can visualise zarr-based files too. This means you don’t need any additional tools or download the files to visually inspect your results.
  • Workflows: Nextflow and KNIME workflows with popular use cases have been wrapped as Galaxy tools to facilitate their use and accessibility, making them available in the Workflow Hub.

Since Galaxy is a workflow management system, you can use any of the tools available there in any order as part of a broader pipeline. To have access to the compute infrastructure in the available public servers, you just need to have a Galaxy account. Galaxy accounts are free, anyone can sign up and then get access to storage and compute power to play with your data.

Do you want to help shape this community resource? Further updates will be discussed at Euro-BioImaging’s FAIR Image Data Workflows Expert Group, led by Beatriz Serrano-Solano and Anne Fouilloux. They meet every3rd Wednesday of the month at 4 pm CE(S)T. Write to info@eurobioimaging.eu to join.

Read the full article about the Hackathon and its outputs on the Galaxy Community Hub: https://galaxyproject.org/news/2024-03-08-hackathon-imaging/

"Image Analysis in Galaxy" hackathon was held from February 26th to March 1st, 2024, at the University of Freiburg (Germany). Co-organised by Euro-BioImaging and NFDI4BIOIMAGE, the event aimed to enhance image analysis capabilities and workflows within the Galaxy platform.

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