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Add Galaxy as a BioImage Model Zoo community partner #25

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B0r1sD opened this issue Nov 6, 2024 · 2 comments
Open

Add Galaxy as a BioImage Model Zoo community partner #25

B0r1sD opened this issue Nov 6, 2024 · 2 comments
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BHEU24 Has been worked on at the BHEU2024 investigation This issue involves some search/research tools dev This issue involves tool development

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@B0r1sD
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B0r1sD commented Nov 6, 2024

BioImage.IO - a collaborative effort to bring AI models to the bioimaging community.

They have already defined a way of working to integrate different communities into the Zoo.

Usually, a community partner is an organization, a company, a research group, or a software team (of one or more) that can consume and/or produce resources of the BioImage.Io model zoo. Additionally, most partners continuously and openly contribute resources of their own. The first community partners represent open source consumer software of BioImage.IO (e.g. ilastik, Fiji, deepImageJ, ZeroCostDL4Mic, StarDist).

This looks like a simlar integration to 'data sources': a direct link between a Galaxy tool and BMZ's database to fluidly get data+models and contribute the other way round.

Documentation from BMZ about what it is, how it works,...: https://bioimage.io/docs/#/guides/community-partners-guide

First iteration will be exploring this possibility and creating the issue in their repo.

@B0r1sD B0r1sD self-assigned this Nov 6, 2024
@kostrykin kostrykin added this to BH2024 Nov 6, 2024
@kostrykin kostrykin moved this to Unassigned - Tool & Galaxy developers in BH2024 Nov 6, 2024
@kostrykin
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It would be cool to connect that integration to the BMZ model tool: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/bioimage_inference/bioimage_inference/2.4.1+galaxy0

@kostrykin kostrykin added tools dev This issue involves tool development investigation This issue involves some search/research labels Nov 7, 2024
@B0r1sD
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B0r1sD commented Nov 7, 2024

Request submitted: bioimage-io/collection#105

@kostrykin kostrykin added the BHEU24 Has been worked on at the BHEU2024 label Nov 8, 2024
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Labels
BHEU24 Has been worked on at the BHEU2024 investigation This issue involves some search/research tools dev This issue involves tool development
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