Glencoe: Synchronizing the data science workflow with data management at scale

Glencoe Software presents the omero2pandas package, designed to integrate with popular Python data science tools and enable analysis workflows which utilize tabular data stored on an OMERO server.

The vast quantities of data generated by scientists necessitate efficient management and analysis solutions to aid discovery and understanding of complex biological processes. OMERO and OMERO Plus are powerful image data management platforms developed by the Open Microscopy Environment (OME) and Glencoe Software, specifically designed for handling life sciences data, including experimental metadata and analytics.

Python has become a popular choice for data manipulation, analysis, and visualization due to its extensive catalogue of third-party libraries, many of which are tailored to the scientific community. This poster, originally presented at JupyterCon 2023, presents the omero2pandaspackage, designed to integrate with popular Python data science tools and enable analysis workflows which utilize tabular data stored on an OMERO server.

The focal point of this presentation is the application of omero2pandas in performing multiplexed digital pathology analysis using unsupervised clustering. These analyses, conducted within a Jupyter notebook environment, underscore the potential of this package to handle complex biomedical data and contribute to the expanding field of digital pathology.