Import only one subsampling of a BigDataViewer pyramidal file in OMERO?

Hello everyone,

Some users at our facility are asking if there is a way to upload only one of the subsampled versions from a pyramidal file (e.g. BigDataViewer .hdf5) to OMERO via the OMERO.insight client ?

All the best,
Claire

Hi Claire (@stoffelc ),

I’m not familiar with omero, unfortunately, but I can help you export just one of the subsampled versions to another format that you / omero can deal with, and maybe that’s an o-k workaround for you. (?)

You can open one of the subsampled levels in the bdv .hdf5 with fiji with:
File > Import > N5

This window will pop up (see below). If you and choosing the hdf5 file, the levels inside the file should be displayed, also something like the below. I’ve selected the downsampled by 4 version, which is in the “group” : t00000/s00/2/cells. Press ok, and that level should open in Fiji, then you can do what you please with it.

I bet you can achieve something similar with File > Import > HDF5.. also.

Hopefully that’s clear, but do post back if it’s not,
John

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