Jean‐Marie Burel
A5076169286- Cell Image Analysis Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Research Data Management Practices
- Scientific Computing and Data Management
- Biomedical Text Mining and Ontologies
- Single-cell and spatial transcriptomics
- Geometric Analysis and Curvature Flows
- Geometric and Algebraic Topology
- AI in cancer detection
- Mathematical Dynamics and Fractals
- Advanced Fluorescence Microscopy Techniques
- Algebraic Geometry and Number Theory
- Usability and User Interface Design
- Digital Imaging for Blood Diseases
- Image Processing Techniques and Applications
- Underwater Vehicles and Communication Systems
- Ethics and Legal Issues in Pediatric Healthcare
- Elasticity and Material Modeling
- Medical Image Segmentation Techniques
- Mathematical Analysis and Transform Methods
- Contact Mechanics and Variational Inequalities
- Geometry and complex manifolds
- Gene expression and cancer classification
- Spacecraft Design and Technology
- Holomorphic and Operator Theory
University of Dundee
2007-2023
Institute of Molecular and Cell Biology
2023
Université de Bretagne Occidentale
2001-2015
Wellcome Trust
2007-2012
Lund University
2004
Institute of Mathematical Sciences
2003
Laboratoire de Mathématiques d'Orsay
2001
Institut de Recherche de l’École Navale
1999
Data sharing is important in the biological sciences to prevent duplication of effort, promote scientific integrity, and facilitate disseminate discovery. Sharing requires centralized repositories, submission utility these resources require common data formats. This particularly challenging for multidimensional microscopy image data, which are acquired from a variety platforms with myriad proprietary file formats (PFFs). In this paper, we describe an open standard format that have developed...
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 Open Microscopy Environment (OME) defines a data model and software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations image analysis results. OME is designed support high-content cell-based screening well traditional applications. Data Model, expressed Extensible Markup Language (XML) realized database, both extensible self-describing, allowing it meet emerging needs.
The main goals and challenges for the life science communities in Open Science framework are to increase reuse sustainability of data resources, software tools, workflows, especially large-scale data-driven research computational analyses. Here, we present key findings, procedures, effective measures recommendations generating establishing sustainable resources based on collaborative, cross-disciplinary work done within EOSC-Life (European Cloud Life Sciences) consortium. Bringing together...
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...
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...
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
Let ${\cal F}$ be an oriented conformal foliation of connected, totally geodesic and 1-dimensional leaves in $\mathbb{R}^{n+1}$. We prove that if $n\geq 3$ then the Gauss map $\phi{:}\,\,U\,{\to}\,S^n$ is a non-constant $n$-harmonic morphism only it radial projection.
Academic scientific software development projects aim to provide valuable research tools aid the community in process of discovery. The need for those meet wider expectations usability and good user experience design is critical success; however nature academic e-science means they are often constrained by too narrow an understanding potential base, a focus on at expense broad research. We introduce concept Project Community as way addressing these limitations capacity support effective...