A5020385687- Cell Image Analysis Techniques
- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Pickering emulsions and particle stabilization
- Image Processing Techniques and Applications
- Advanced Fluorescence Microscopy Techniques
- Gene expression and cancer classification
- Cancer, Hypoxia, and Metabolism
- Radiomics and Machine Learning in Medical Imaging
- Photoacoustic and Ultrasonic Imaging
- Biomedical Text Mining and Ontologies
- Plant Molecular Biology Research
- Plant Reproductive Biology
- Medical Image Segmentation Techniques
- Microtubule and mitosis dynamics
- AI in cancer detection
- Single-cell and spatial transcriptomics
- Surfactants and Colloidal Systems
- Plant Stress Responses and Tolerance
- Cellular Mechanics and Interactions
- 3D Printing in Biomedical Research
- Saffron Plant Research Studies
- Plant and Biological Electrophysiology Studies
- Digital Radiography and Breast Imaging
- Polymer Foaming and Composites
University of Dundee
2014-2023
Institute of Molecular and Cell Biology
2023
Harvard University Press
2011-2012
Harvard University
2011-2012
Laboratoire de Physique de l'ENS
2007-2011
Centre National de la Recherche Scientifique
2007-2008
Abstract The rapid pace of innovation in biological imaging and the diversity its applications have prevented establishment a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF HDF5 with next-generation file format Zarr will satisfy majority use cases bioimaging. Critically, common metadata used all these vessels can deliver truly findable, accessible, interoperable reusable bioimaging data.
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...
The division of eukaryotic cells involves the assembly complex cytoskeletal structures to exert forces required for chromosome segregation and cytokinesis. In plants, empirical evidence suggests that tensional within cytoskeleton cause divide along plane minimizes surface area cell plate (Errera’s rule) while creating daughter equal size. However, exceptions Errera’s rule cast doubt on whether a broadly applicable can be formulated plant division. Here, we show selection competition between...
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...
Quantitative fluorescent speckle microscopy (QFSM) is a live-cell imaging method to analyze the dynamics of macromolecular assemblies with high spatial and temporal resolution. Its greatest successes were in analysis actin filament adhesion context cell migration microtubule interphase meiotic/mitotic spindle. Here, focus on former application illustrate procedures FSM computational image processing that extracts quantitative information from these experiments. QFSM advantageous over other...
Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to diversity of experimental protocols non-standardized output formats. In addition, typically are open for reuse. Making data Findable, Accessible, Interoperable, Reusable (FAIR) will enable meta-analysis, integration, mining. Standardized formats controlled vocabularies essential building suitable...
OPINION article Front. Plant Sci., 09 October 2014Sec. Development and EvoDevo https://doi.org/10.3389/fpls.2014.00538
Summary Biological imaging is one of the most innovative fields in modern biological sciences. New modalities, probes, and analysis tools appear every few months often prove decisive for enabling new directions scientific discovery. One feature this dynamic field need to capture types data structures. While there a strong drive make Findable, Accessible, Interoperable Reproducible (FAIR 1 ), rapid rate innovation impedes unification adoption standardized formats. Despite this, opportunities...
ABSTRACT Spindle length varies dramatically across species and during early development to segregate chromosomes optimally. Both intrinsic factors, such as regulatory molecules, extrinsic cytoplasmic volume, determine spindle scaling. However, the properties that govern shape whether these features can be modulated remain unknown. Here, we analyzed quantitatively how molecular players which regulate microtubule dynamics control kinetics of formation shape. We find that, in absence Clasp1...
The link between the rheology of 3D aqueous foam and adhesion neighboring bubbles is tested by confronting experiments at two different length scales. On one hand, dynamics are probed measuring how shape in contact changes as their center-to-center distance modulated. other linear viscoelastic behavior prepared with same soapy solution characterized its complex shear modulus. To connect sets data, we present a model viscoelasticity taking into account bubble adhesion.
Digital imaging is now used throughout biological and biomedical research to measure the architecture, composition dynamics of cells, tissues organisms.The many different technologies create data in formats.This diversity formats
Abstract Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited due to diversity of experimental protocols non-standardised output formats. In addition, typically are open for reuse. Making data Findable, Accessible, Interoperable, Reusable (FAIR) will enable meta-analysis, integration, mining. Standardised formats controlled vocabularies essential building suitable...
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...