🟡Newsletter - August 2025
Montly Newsletter
Newsletter – September 2025
Monthly Newsletter Labguru for Reproducibility and Metadata in Bioimaging
Disclaimer The views expressed here are my own in my professional capacity as a Data Steward and Research Data Manager. They do not necessarily represent the official positions of the Novo Nordisk Foundation Center for Stem Cell Medicine – reNEW.
Introduction
Digital tools for managing experiments are no longer optional; they are becoming essential for modern research. Labguru, an electronic lab notebook (ELN) and laboratory information management system (LIMS), provides a structured environment for capturing experimental details, storing results, and linking data to projects and publications.
At reNEW, Labguru holds particular promise in bioimaging. By systematically recording experimental metadata, protocols, and analytical workflows, Labguru can help ensure that bioimages are stored securely, fully reproducible, and FAIR (Findable, Accessible, Interoperable, Reusable).
Key Challenges in Managing Bioimage Metadata
Fragmented Record-Keeping Metadata about bioimages is often spread across notebooks, emails, and files, making it difficult to reconstruct the full context of an experiment.
Loss of Reproducibility Without structured metadata, repeating experiments or validating results becomes nearly impossible. Key information about samples, microscope settings, or analysis pipelines may be missing.
Data Integration Gaps Bioimage data are increasingly linked to genomics, proteomics, and other omics datasets. Without standardized metadata, cross-comparison and integration are severely limited.
Best Practices and Solutions: Labguru in Action
Open Access
Supports structured export of protocols and results that can accompany publications.
Facilitates transparent sharing of experimental context alongside datasets.
Open Data
Links bioimage metadata with raw image files in trusted repositories.
Provides a foundation for FAIR-aligned data sharing at reNEW.
Open Methodology
Captures detailed experimental protocols, microscope settings, and analysis steps.
Ensures that workflows can be exactly repeated or critically assessed.
Open Source Integration
Allows connection with open-source image analysis tools (e.g., ImageJ, OMERO).
Promotes reproducibility through transparent computational workflows.
Local Context: reNEW and UCPH
At reNEW Copenhagen and the University of Copenhagen, Labguru is being used and adopted to strengthen research practices in bioimaging. Specifically, it supports:
Metadata Standardization: Recording experimental details in a structured format.
Integration with OMERO: Facilitating the movement of bioimages to repositories with enriched metadata.
Collaboration Across Groups: Providing a common platform for researchers to share and validate protocols.
Compliance with UCPH Policies: Aligning with institutional requirements for data management and FAIR compliance.
Practical Recommendations
Adopt Labguru as a Central ELN – Consolidate protocols, results, and metadata in one platform.
Link Labguru to OMERO and Repositories – Ensure bioimages and metadata remain connected.
Use Labguru for Protocol Versioning – Track changes over time to support reproducibility.
Encourage Group-Wide Adoption – Ensure consistent metadata capture across reNEW labs.
Incorporate Metadata into DMPs – Make metadata standards a planned component of projects.
Looking Ahead
Labguru offers reNEW an opportunity to set new reproducibility and metadata-driven research standards. By embedding Labguru in everyday bioimaging workflows, we can ensure that our datasets are stored, understood, trusted, and reusable. In the long term, this position reNEW at the forefront of transparent, reproducible, and FAIR research in the biomedical sciences.
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