OMERO Upload from Aperio Slide Scanner

I wanted to inquire about how you could directly upload scanned while slide images captured with the Leica Aperio AT Turbo to an OMERO server?

@awald2024 to clarify your expectations, I assume the workflow would be to save whole slide images on disk and have these automatically imported into an OMERO.server? If so, something worth looking into would be the OMERO.dropbox functionality.

The primary question though is whether Leica Aperio AT Turbo saves its data in a file format compatible with OMERO. Form the list of supported formats, the SVS format would be my expectation.

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Thanks! Yes it’s SVS format. I was hoping that the files could be directly written/saved to the server. Is that possible or would I have to save to a disk first?

Hi @awald2024,

What type of API would you be looking to use for this?

Likely the best example we have at the moment is in the incubator omero_webimport project. It shouldn’t be too difficult to define a file generator (“folder_gen”) which works from memory rather than from disk.

All the best,
~Josh

Thanks! My apologies for the naive question as I’m quite new to all this. So would I have to code something to make this work? I wouldn’t be able to put the server address path in the microscope settings when running my experiment and have it upload as if it were a USB or something?

Hi @awald2024,

No need to apologize. You’re right that the OME team doesn’t provide the type of solution you’re looking for. I assume it’s possible to code something to stream from the scanner system, but it depends on what APIs are provided, and I don’t have any experience with that.

From our point-of-view, it would take a dedicated adapter for every microscope in order to enable this, which is something we can’t support with public funding. We’d love to help others make it happen though!

Alternatively, perhaps someone else on the forums has already built something similar and if so, they might speak up here.

All the best,
~Josh

P.S. Another option that may work fairly similarly is if you could share a filesystem between the two systems. If this is of interest, let us know and we can provide information.