New blog post on the Helmholtz Metadata Collaboration 2024

content/blog/2024-11-galaxy-imaging-fair-pipelines/index.md

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+---
+date: '2024-11-08'
+title: "Report from the Helmholtz Metadata Collaboration Conference (HMC) 2024"
+tease: "Galaxy imaging and RDM workflows were presented at the HMC 2024"
+authors: "Riccardo Massei"
+tags: [fair, imaging, pipelines, workflow]
+---
+
+## The Helmholtz Metadata Conference (HMC) 2024
+
+The Helmholtz Metadata Collaboration (HMC) focuses on enhancing research
+data quality through metadata, implementing this approach throughout the 
+entire organisation. Its primary goal is to make the extensive research 
+data produced by Helmholtz Centres findable, accessible, interoperable, 
+and reusable (FAIR) for the scientific community. This year’s Helmholtz 
+Metadata Conference (HMC) was held virtually in Gather Town from November 
+4th to 6th. The event targeted scientists, data professionals, software developers,
+and anyone engaged with metadata. Sessions covered a range of topics, 
+including metadata management, ontologies, metadata schemas and formats, 
+semantics, standardisation, and workflows.
+
+![HMC_logo.png](HMC_logo.png)
+
+## Building FAIR Bioimage Pipelines with Galaxy
+In the “workflow” session, I presented the application of Galaxy to develop 
+FAIR analysis pipelines for metadata annotation and image management in 
+high-content screening (HCS) bioimaging. In fact, Galaxy workflows enhance 
+data FAIRness by allowing annotation, collaboration, and public sharing. 
+Additionally, Galaxy tools are transparent, meaning they can be easily 
+inspected within the Galaxy Tool Shed, providing a clear view of their 
+structure.
+
+![pipeline_ip.png](pipeline_ip.png)
+
+## Integrating OMERO and Galaxy
+During the conference, I discussed integrating OMERO’s upload and image 
+annotation features with Galaxy’s image analysis workflows. 
+This integration enables images to be automatically enriched with metadata 
+(e.g., key-value pairs, tags, raw data, regions of interest) and uploaded 
+to a user-defined OMERO server using a new OMERO tool suite developed in 
+Galaxy. Currently, the suite offers tools for image and ROI uploads, 
+metadata enrichment, and data filtering or retrieval, making it simple 
+to transfer data and metadata to an OMERO instance.
+
+![img.png](omero_pipeline.png)
+
+
+## Combining Image Processing and Data Management in One Workflow
+Image processing can be added to OMERO workflows. Users can retrieve
+images from a local server and perform image analyses, such as annotation,
+segmentation, or background subtraction. Galaxy is a powerful tool for 
+image analysis, integrating popular software like CellProfiler and connecting 
+with cloud services like OMERO and the IDR. This integration allows for 
+efficient access to and management of image data, which is invaluable in 
+bioimaging. Automated pipelines streamline the handling of complex metadata,
+ensuring data integrity and fostering interdisciplinary collaboration. 
+This approach not only boosts the efficiency of HCS bioimaging but 
+also aligns with the scientific community’s FAIR principles, driving 
+scientific discovery and innovation forward.
+
+
+The presentation was shared on [Zenodo](https://zenodo.org/records/14044640)