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# System prepended metadata

title: 2023-01-20 EBI Bioimage archive + spatial data
tags: [ebi, meeting, spatialdata, scverse, ome-ngff]

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tags: [spatialdata, ebi, scverse, ome-ngff, meeting]
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# 2023-01-20 EBI Bioimage archive + spatial data

*Attendees*: Isaac Virshup, Giovanni Palla, Luca Marconato, Josh Moore, Mathew Hartley

# Minutes

* Mathew Hartley – EBI based, working on https://www.ebi.ac.uk/biostudies/BioImages/studies
* Presentation from Luca
* Timeline for ome-ngff
    * 6 months on 0.5?
    * Java implementation of tables, not done
        * Backend for java (mobie) needs work, may not be resourced
* Bioimage archive
    * New EBI data resource – started 2019, but had people in 2021
    * Deposition database for image from "any modality"
        * Some more specialized resources for specific techs, but archive will post to it
    * Image data from publications, though maybe also 
    * Kinds of data
        * Raw is big, but processed can be easier to share
        * If it's standardized processing, it can be okay to omit 
    * Formats allowed:
        * Currently not, in future more
    * Collaborations with curated collections
        * Added value databases
        * Like SRA vs ebi expression atlas
    * We can submit data in our format
    * Storage systems
        * Big slow object storage system
            * Does not seem to work well with NGFF
            * Archival
        * Fast storage is s3 embassy
        * NGFF is typically exported to
    * Link from Josh as temporary resource https://uk1s3.embassy.ebi.ac.uk/idr/browser.html
* Hosting for data
* Use case?
    * Would like to have fast storage, not much copying/ re-hosting
    * But of course there are limitations here
* Q: from matt
    * Are there restrictions on chunking?
* Following up with single cell expression atlas people?
* Josh – AI for Life meeting?
    * Is this relevant there
* Follow up from our side:
    * Get them data in our format (though they have some)

* Questions
    * Working with Tong?
    * In contact with vitessce?
    * Vision for usage?