A5072188263- Cell Image Analysis Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Plant Reproductive Biology
- Single-cell and spatial transcriptomics
- Microbial Community Ecology and Physiology
- AI in cancer detection
- Plant Molecular Biology Research
- Advanced Fluorescence Microscopy Techniques
- Plant and Biological Electrophysiology Studies
- Light effects on plants
- Magnetic and Electromagnetic Effects
- Image Processing Techniques and Applications
- Wastewater Treatment and Nitrogen Removal
- Botanical Research and Applications
- Microfluidic and Capillary Electrophoresis Applications
- Bacterial biofilms and quorum sensing
- Plant Stress Responses and Tolerance
- thermodynamics and calorimetric analyses
- Edcuational Technology Systems
- Photosynthetic Processes and Mechanisms
- Polysaccharides and Plant Cell Walls
- Biomedical Text Mining and Ontologies
- Plant Physiology and Cultivation Studies
- Photoacoustic and Ultrasonic Imaging
University of Dundee
2015-2023
Institute of Molecular and Cell Biology
2023
Helmholtz Centre for Environmental Research
2004-2007
University of Freiburg
2000-2003
Czech Academy of Sciences, Institute of Physiology
2000
Czech Academy of Sciences
2000
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 institutes across diverse modalities facing these have designed specification process (OME-NGFF) address needs. This paper brings together wide range those members describe cloud-optimized itself-OME-Zarr-along with tools data resources available today increase FAIR access remove barriers...
High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated linked to produce set "final" results. These different include images, reagents, protocols, analytic output, phenotypes, all which stored, made accessible for users, scientists, collaborators where appropriate the wider community. The OME Consortium has built several open source tools managing, linking sharing...
Imaging data are used in the life and biomedical sciences to measure molecular structural composition dynamics of cells, tissues, organisms. Datasets range size from megabytes terabytes usually contain a combination binary pixel metadata that describe acquisition process any derived results. The OMERO image management platform allows users securely share datasets according specific permissions levels: can be held privately, shared with set colleagues, or made available via public URL. Users...
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 institutes across diverse modalities facing these have designed specification process (OME-NGFF) address needs. This paper brings together wide range those members describe cloud-optimized itself -- OME-Zarr along with tools data resources available today increase FAIR access remove...
The Open Microscopy Environment (OME) has built and released Bio-Formats, a Java-based proprietary file format conversion tool OMERO, an enterprise data management platform under open source licenses. In this report, we describe new versions of Bio-Formats OMERO that are specifically designed to support large, multi-gigabyte or terabyte scale datasets routinely collected across most domains biological biomedical research. Bio- Formats reads image directly from native formats, bypassing the...
ABSTRACT In this study, the feasibility of fluorescence lifetime imaging (FLIM) for measurement RNA:DNA ratios in microorganisms was assessed. The a nucleic acid-specific probe (SYTO 13) used to directly measure ratio inside living bacterial cells. vitro, SYTO 13 showed shorter lifetimes DNA solutions than RNA solutions. Growth experiments with monocultures were performed liquid media. results demonstrated suitability measuring growth-phase-dependent Escherichia coli reflected known changes...
Conventional confocal laser scanning microscopy uses continuous wave visible or UV lasers for one-photon excitation and imaging. These instruments are now enhanced with pulsed infrared allowing two-photon excitation. With the appropriate technical setup may be used intensity imaging lifetime Both of these techniques have specific advantages if compared Despite this fact, to date mainly has been employed in microbial ecology. In review potential is discussed, using examples from cell biology...
ABSTRACT The apical meristem of the short‐day plant Chenopodium rubrum responds to photoperiodic flower induction with specific changes pH and Ca 2+ patterning immediately after inductive dark span. red–far‐red reversibility in response night break treatments was measured order distinguish between effect prolonged span per se induction. In addition, C. compared long‐day murale. visualized using fluorescent probe carboxy SNARF‐1. Calcium ion concentrations were studied a combination ‐probes...
Background COVID-19 shifted Indonesian education to remote learning. The Gadjah Mada University (UGM) Faculty of Medicine Public Health and Nursing (UGM FMPHN) struggled with studying tumor images remotely due resource shortages. In parallel, the Dundee's (UoD) OME team created OMERO for image management, inspiring UGM use develop GamaPath web-based viewing. This report details its implementation, effectiveness, potential expansion practical sessions workshops in Indonesia. Methods Teaching...
Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage analysis facilities lacking, as standards for sharing image data results. While the open FITS format is ubiquitous astronomy, astronomical shares many with imaging, including need to share large sets using secure, cross-platform APIs, scalable applications processing visualization. The Open Microscopy Environment (OME) an open-source software...