David Gault
University of Dundee
8 Papers
1 Citations
David Gault is an academic researcher from University of Dundee. The author has contributed to research in topics: File format & Open format. The author has an hindex of 3, co-authored 6 publications.
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Papers
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies.
Josh Moore,Chris Allan,Sébastien Besson,Jean-Marie Burel,Erin Diel,David Gault,Kevin Kozlowski,Dominik Lindner,Melissa Linkert,Trevor Manz,William J. Moore,Constantin Pape,Christian Tischer,Jason R. Swedlow +13 more
TL;DR: In this paper, the authors propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging.
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OME-Zarr: a cloud-optimized bioimaging file format with international community support.
Josh Moore,Daniela Basurto-Lozada,Sébastien Besson,John A. Bogovic,Jordão Bragantini,Jean-Marie Burel,Xavier Casas Moreno,Gustavo de Medeiros,Erin E. Diel,David Gault,Satrajit S. Ghosh,Ilan Gold,Yaroslav O. Halchenko,M. Hartley,Dave Horsfall,Mark Keller,Mark Kittisopikul,Gabor Kovacs,Aybuke Kupce Yoldas,Koji Kyoda,Tong Li,Prisca Liberali,Dominik Lindner,Melissa Linkert,Joel Lüthi,Jeremy Maitin-Shepard,Trevor Manz,Luca Marconato,Matthew Mccormick,Merlin Lange,Khaled Mohamed,William J. Moore,Nils Norlin,Wei Ouyang,Bugra Özdemir,Giovanni Palla,Constantin Pape,Lucas Pelkmans,Tobias Pietzsch,Stephan Preibisch,M. Julieta Del Prete,Norman Rzepka,Sameeul B. Samee,Nicholas J. Schaub,Hythem Sidky,Ahmet Can Solak,David R. Stirling,Jonathan Striebel,Christian Tischer,Daniel M. Toloudis,I H Virshup,Petr Walczysko,Alan M. Watson,Erin Weisbart,Frances Wong,Kevin A. Yamauchi,Omer Ali Bayraktar,Beth A. Cimini,Nils Gehlenborg,Muzlifah Haniffa,Nathan Hotaling,Shuichi Onami,Loic Royer,Stephan Saalfeld,Oliver Stegle,Fabian J. Theis,Jason R. Swedlow +66 more
TL;DR: A wide range of community members are brought together to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process.
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Building bridges between cellular and molecular structural biology.
Ardan Patwardhan,Robert Brandt,Sarah J. Butcher,Lucy M. Collinson,David Gault,Kay Grünewald,Corey W. Hecksel,Juha T. Huiskonen,Andrii Iudin,Martin L. Jones,Paul K. Korir,Abraham J. Koster,Ingvar Lagerstedt,Catherine L. Lawson,David N. Mastronarde,Matt McCormick,Helen Parkinson,Peter B. Rosenthal,Stephan Saalfeld,Helen R. Saibil,Sirarat Sarntivijai,Irene Solanes Valero,Sriram Subramaniam,Jason R. Swedlow,Ilinca Tudose,Martyn Winn,Gerard J. Kleywegt +26 more
TL;DR: A workshop that discussed how to integrate structural data from a range of public archives identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and theDevelopment of tools to support the annotation of biological structures.
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.
The Open Microscopy Environment: open image informatics for the biological sciences
Colin Blackburn,Chris Allan,Sébastien Besson,Jean-Marie Burel,Mark Carroll,Richard K. Ferguson,Helen Flynn,David Gault,Kenneth Gillen,Roger Leigh,Simone Leo,Simon Li,Dominik Lindner,Melissa Linkert,Josh Moore,William J. Moore,B. Ramalingam,E. Rozbicki,Gabriella Rustici,Aleksandra Tarkowska,Petr Walczysko,Eleanor Williams,Jason R. Swedlow +22 more
TL;DR: OMERO’s model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies.