This module invites you to learn about BioImage Archive, an image data repository for light microscopy.
The BioImage Archive stores and distributes biological images that are useful to life sciences researchers. Its development will provide data archiving services to the broader bioimaging database community. This includes added value bioimaging data resources such as EMPIAR, Cell-IDR and Tissue-IDR.
Presenter: Matthew Hartley, EMBL-EBI, United Kingdom
Introduction to BioImage Archive in the form of presentation slides.
Presenter: Teresa Zulueta-Coarasa, EMBL-EBI, United Kingdom
Access BioImage Archive using the link above.
Introduction to BioImage Archive: Global BioImaging YouTube channel
Submitting data to the BioImage Archive: Euro-BioImaging Communication YouTube channel
This module invites you to learn about the Electron Microscopy Public Image Archive, an image data repository for electron microscopy.
EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw images underpinning 3D cryo-EM maps and tomograms (themselves archived in EMDB). EMPIAR also accommodates 3D datasets obtained with volume EM techniques and soft and hard X-ray imaging, all on scales from molecules to organisms. All data archived in EMPIAR can be re-used freely without any conditions or restrictions ("CC0" license model). The purpose of EMPIAR is to provide easy access to state-of-the-art data to facilitate methods development, validation and re-use, e.g., for Machine Learning applications. EMPIAR data is also used for training and teaching purposes and as part of community challenges.
Presenter: Gerard Kleywegt, EMBL-EBI, United Kingdom
Introduction to EMPIAR in the form of presentation slides.
Developed by: Andrii Iudin and Ardan Patwardhan, EMBL-EBI, United Kingdom
Access and learn more about EMPIAR at the link above.
Introduction to EMPIAR: Global BioImaging YouTube channel
EMPIAR course: EMBL-EBI website
This module invites you to learn about Image Data Resource, an image repository for light microscopy data.
Image Data Resource (IDR) is a public repository of image datasets from published scientific studies, where the community can submit, search and access highly annotated datasets. The IDR makes datasets that have never been previously accessible publicly available, allowing the community to search, view, mine and even process and analyze large, complex, multidimensional life sciences image data. Sharing of image data promotes the validation of experimental methods and scientific conclusions, the comparison with new image data obtained by the global scientific community, and enables data reuse by developers of new image analysis and processing tools.
Presenter: Petr Walczysko, Open Microscopy Environment, University of Dundee, Dundee, Scotland
Introduction to the IDR in the form of presentation slides.
Presenter: Petr Walczysko, Open Microscopy Environment, University of Dundee, Dundee, Scotland
Access and learn more about IDR at the link above.
Introduction to IDR: Global BioImaging YouTube channel
IDR Workshop: Global BioImaging YouTube channel
This module invites you to learn about OMERO, an image data management software that stores all of your images in secure central repository.
OMERO, developed by OME, is an open source, enterprise software platform for image data management and analysis. OMERO handles all of the images in a secure central repository. Microscope images and metadata can be viewed, analyzed, and shared from anywhere you have internet access. Images can be worked on from the desktop application (Windows, Mac, and Linux), from a browser, or 3rd party software. Currently, over 150 image file formats are supported, including all major microscope formats.
Presenter: Jason Swedlow, Open Microscopy Environment, University of Dundee, Dundee, Scotland
Introduction to OMERO
IDR and BioImage Archive
Bio-Formats
Presenter: Petr Walczysko, Open Microscopy Environment, University of Dundee, Dundee, Scotland
Brief introduction to the OMERO in the form of presentation slides.
Demonstration of how to import images to OMERO.
Presenter: Petr Walczysko, Open Microscopy Environment, University of Dundee, Dundee, Scotland
Presenter: Petr Walczysko, Open Microscopy Environment, University of Dundee, Dundee, Scotland
Presenter: Petr Walczysko, Open Microscopy Environment, University of Dundee, Dundee, Scotland
Demonstration of how to use OMERO.figure to create publication quality figures.
Presenter: Petr Walczysko, Open Microscopy Environment, University of Dundee, Dundee, Scotland
Download and learn more about OMERO at the link above.
This project has been made possible in part by a grant from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation.
