OMERO: flexible, model-driven data management for experimental biology

C Allan, JM Burel, J Moore, C Blackburn, M Linkert… - Nature …, 2012 - nature.com
Data-intensive research depends on tools that manage multidimensional, heterogeneous
datasets. We built OME Remote Objects (OMERO), a software platform that enables access to …

Metadata matters: access to image data in the real world

M Linkert, CT Rueden, C Allan, JM Burel… - Journal of Cell …, 2010 - rupress.org
Data sharing is important in the biological sciences to prevent duplication of effort, to promote
scientific integrity, and to facilitate and disseminate scientific discovery. Sharing requires …

[HTML][HTML] OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies

…, E Diel, D Gault, K Kozlowski, D Lindner, M Linkert… - Nature …, 2021 - nature.com
The rapid pace of innovation in biological imaging and the diversity of its applications have
prevented the establishment of a community-agreed standardized data format. We propose …

[HTML][HTML] Publishing and sharing multi-dimensional image data with OMERO

…, K Gillen, R Leigh, S Li, D Lindner, M Linkert… - Mammalian …, 2015 - Springer
Imaging data are used in the life and biomedical sciences to measure the molecular and
structural composition and dynamics of cells, tissues, and organisms. Datasets range in size …

Pex19p, a farnesylated protein essential for peroxisome biogenesis

K Götte, W Girzalsky, M Linkert… - … and Cellular Biology, 1998 - Taylor & Francis
We report the identification and molecular characterization of Pex19p, an oleic acid-inducible,
farnesylated protein of 39.7 kDa that is essential for peroxisome biogenesis in …

[HTML][HTML] OME-Zarr: a cloud-optimized bioimaging file format with international community support

…, T Li, P Liberali, D Lindner, M Linkert… - Histochemistry and Cell …, 2023 - Springer
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 …

Bringing open data to whole slide imaging

…, R Leigh, M Linkert, C Allan, JM Burel, M Carroll… - European Congress on …, 2019 - Springer
Faced with the need to support a growing number of whole slide imaging (WSI) file formats,
our team has extended a long-standing community file format (OME-TIFF) for use in digital …

[HTML][HTML] Metadata management for high content screening in OMERO

…, H Flynn, K Gillen, R Leigh, D Lindner, M Linkert… - Methods, 2016 - Elsevier
High content screening (HCS) experiments create a classic data management challenge—multiple,
large sets of heterogeneous structured and unstructured data, that must be …

OME-NGFF: scalable format strategies for interoperable bioimaging data

…, E Diel, D Gault, K Kozlowski, D Lindner, M Linkert… - BioRxiv, 2021 - biorxiv.org
Biological imaging is one of the most innovative fields in the modern biological sciences. New
imaging modalities, probes, and analysis tools appear every few months and often prove …

OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale

…, M Linkert, C Blackburn, M Carroll… - Medical Imaging …, 2015 - spiedigitallibrary.org
The Open Microscopy Environment (OME) has built and released Bio-Formats, a Java-based
proprietary file format conversion tool and OMERO, an enterprise data management …