Biology subjects
Publications and source records attributed to Burel, J.-M..
We introduce the IDR searcher, an open-source search engine designed to ease the exploration of datasets hosted in public bioimaging resources. The application offers a fast, efficient, cost-effective solution for datasets discovery and has the potential to address current disparities in finding quality datasets for exploratory research and to provide the foundation for cross-resource search.
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members 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. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.
Digital imaging is now used throughout biological and biomedical research to measure the architecture, composition and dynamics of cells, tissues and organisms. The many different imaging technologies create data in many different formats. This diversity of data formats arises because the creation of common, cross-domain data standards is difficult and the pace of innovation challenges the durability of any defined standard and the implementation of data stewardship principles such as FAIR1. The Open Microscopy Environment (OME; http://openmicroscopy.org) has therefore developed the OME Data Model, an open, extensible specification for imaging metadata, that supports metadata related to an imaging experiment, data acquisition and any derived analytic results2-4. The OME Data Model has been implemented in OME-XML so that metadata can be stored and accessed by any sof ...