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High-content screening (HCS) workflows for FAIR image data management with OMERO.

Riccardo Massei^1,2,3, Wibke Busch⁴, Beatriz Serrano-Solano⁵

¹Research Data Management - RDM, Helmholtz Centre for Environmental Research (UFZ), Permoserstraße 15, 04318, Leipzig, Germany. riccardo.massei@ufz.de.

Scientific Reports

|May 9, 2025

Summary

This summary is machine-generated.

High-content screening (HCS) bioimaging generates vast data. Workflow Management Systems (WMS) with OMERO streamline HCS data management, ensuring reproducible and efficient image analysis.

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Area of Science:

Bioimaging
Data Management
Scientific Workflow Automation

Background:

High-content screening (HCS) bioimaging generates large datasets, posing significant data management challenges.
Effective management of HCS data, including images, reagents, and analysis outputs, is crucial for reproducible research.
Current data management practices can be inefficient and prone to errors, hindering data sharing and collaboration.

Purpose of the Study:

To demonstrate reusable semi-automatic workflows for HCS bioimaging data management using Workflow Management Systems (WMS) and OMERO.
To showcase the transition from local file-based storage to an automated and agile data management framework.
To improve the efficiency, effectiveness, and reproducibility of HCS image data management.

Main Methods:

Development of three distinct semi-automatic workflows utilizing Workflow Management Systems (WMS).
Integration of WMS with the OMERO image data management platform.
Application of workflows for structured and reproducible image data transfer and management.

Main Results:

Successful transition from local file storage to an automated data management framework.
Demonstrated reduction in human error and improved efficiency in HCS data handling.
Enhanced data consistency and reproducibility through structured image transfer across locations.

Conclusions:

Workflow Management Systems offer a robust solution for managing large-scale HCS bioimaging data.
Semi-automatic workflows using WMS and OMERO improve data management efficiency and reproducibility.
Future work should explore advanced workflows and machine learning integration for automated image analysis.