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Support uploading to Project and Screen objects #10

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Nov 17, 2023
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DavidStirling
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Expands upload support to cover Projects and Screens

@sbesson
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sbesson commented Nov 15, 2023

As we are widening the scope of the objects to which tables can be linked, would it make sense to provisionally add ROI ?

@DavidStirling
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Is it possible to find ROI-linked tables in OMERO.web? I figured for ROI support the approach would be to associate the table with a parent image and have a separate ROI link added to it.

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sbesson commented Nov 15, 2023

Is it possible to find ROI-linked tables in OMERO.web?

Not currently. No objections to draw the line as "anything that gets created/updated/read via omero2pandas must be accessible and manageable via OMERO.web webclient" at least for the time being

@emilroz
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emilroz commented Nov 16, 2023

@sbesson do you have any specific workflows in mind? I think the ROI_Converter_NGFF is linking ROI-type tables to Images. But let us know if there's something specific we should take into account here.

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sbesson commented Nov 16, 2023

I don't have any specific workflow in mind but I was generally thinking tabular data associated to label images. At the moment, the existing tooling links these tables at the Image level but there are ongoing discussions about linking them at the ROI level. This will in turn raise all the management questions via the UI brought by @DavidStirling.

I suggest we do not block this PR on this discussion. Project/Screen tabular annotations are well-established workflows and there is no reason omero2pandas should not be able to handle those.

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Successfully tested the upload_table workflow using both a Project and a Screen target

@sbesson sbesson mentioned this pull request Nov 17, 2023
@emilroz emilroz merged commit a2158f5 into main Nov 17, 2023
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3 participants