Simon Li
University of Dundee
8 Papers
9 Citations
Simon Li is an academic researcher from University of Dundee. The author has contributed to research in topics: Metadata & File format. The author has an hindex of 7, co-authored 8 publications. Previous affiliations of Simon Li include European Bioinformatics Institute.
Chat about Author
Papers
Publishing and sharing multi-dimensional image data with OMERO
Jean-Marie Burel,Sébastien Besson,Colin Blackburn,Mark Carroll,Richard K. Ferguson,Helen Flynn,Kenneth Gillen,Roger Leigh,Simon Li,Dominik Lindner,Melissa Linkert,William J. Moore,B. Ramalingam,E. Rozbicki,Aleksandra Tarkowska,Petr Walczysko,Chris Allan,Josh Moore,Jason R. Swedlow +18 more
TL;DR: The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL.
Metadata management for high content screening in OMERO.
Simon Li,Sébastien Besson,Colin Blackburn,Mark Carroll,Richard K. Ferguson,Helen Flynn,Kenneth Gillen,Roger Leigh,Dominik Lindner,Melissa Linkert,William J. Moore,B. Ramalingam,E. Rozbicki,Gabriella Rustici,Aleksandra Tarkowska,Petr Walczysko,Eleanor Williams,Chris Allan,Jean-Marie Burel,Josh Moore,Jason R. Swedlow +20 more
TL;DR: Repositories integrating multiple image-based studies provide tests of the value of data integration and OMERO and Bio-Formats are open-source tools for data access and management at scale.
53
Bringing Open Data to Whole Slide Imaging.
Sébastien Besson,Roger Leigh,Melissa Linkert,Chris Allan,Jean-Marie Burel,Mark Carroll,David Gault,Riad Gozim,Simon Li,Dominik Lindner,Josh Moore,William J. Moore,Petr Walczysko,Frances Wong,Jason R. Swedlow +14 more
TL;DR: The team has extended a long-standing community file format (OME-TIFF) for use in digital pathology by making use of the core TIFF specification to store multi-resolution representations of a single slide in a flexible, performant manner.
OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale
Josh Moore,Melissa Linkert,Colin Blackburn,Mark Carroll,Richard K. Ferguson,Helen Flynn,Kenneth Gillen,Roger Leigh,Simon Li,Dominik Lindner,William J. Moore,Andrew J. Patterson,Blazej Pindelski,B. Ramalingam,E. Rozbicki,Aleksandra Tarkowska,Petr Walczysko,Chris Allan,Jean-Marie Burel,Jason R. Swedlow +19 more
TL;DR: New versions of Bio-Formats and OMERO are described that are specifically designed to support large, multi-gigabyte or terabyte scale datasets that are routinely collected across most domains of biological and biomedical research.
36
The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination
Eleanor Williams,Josh Moore,Simon Li,Gabriella Rustici,Aleksandra Tarkowska,Anatole Chessel,Simone Leo,Balint Antal,Richard K. Ferguson,Ugis Sarkans,Alvis Brazma,Rafael E. Carazo Salas,Swedlow +12 more
TL;DR: IDR links high-content screening, super-resolution microscopy, time-lapse and digital pathology imaging experiments to public genetic or chemical databases, and to cell and tissue phenotypes expressed using controlled ontologies, facilitating the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies.
10