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 …
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 …
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
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 …
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 …
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 …
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
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 …
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 …
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 …
large sets of heterogeneous structured and unstructured data, that must be …
OME-NGFF: scalable format strategies for interoperable bioimaging data
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 …
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 …
proprietary file format conversion tool and OMERO, an enterprise data management …