[Neuroimaging] Planning for data formats - upcoming journal club

[Joshua Moore (Staff)]

> Thanks - these are strikingly relevant ...



I’d second that! But I (with my OME hat on) would also second Satra said that there are cases & users that will continue to prefer HDF5 and once we’ve worked through the design of NGFF, we’ll likely try to bring the same design to HDF5, keeping the two convertible to one another to support as much of the community as possible.



And for what it’s worth, we also received CZI funding (with my Zarr hat on) for driving imaging forward, and the kind folks at Unidata are doing what they can to have HDF5 & Zarr supported seamlessly through NetCDF. Exciting times.



Happy to discuss further or join the/a call as appropriate.



~Josh



P.S. Sorry if this email breaks the mailing list thread. I’ve only just joined after being kindly pointed to it by Greg Lee.





On Wed, Nov 10, 2021 at 12:22 EST Matthew Brett via Neuroimaging



> On Wed, Nov 10, 2021 at 4:35 PM Thomas Pengo via Neuroimaging <neuroimaging at python.org<https://mail.python.org/mailman/listinfo/neuroimaging>> wrote:

> > I am new to writing to this list but I simply wanted to bring a couple of pointers to related efforts in microscopy. Apologies if this is redundant.

> >

> > Open Microscopy Environment. They started with a data model, in XML. The data model covers data and metadata so initially you could write data and metadata in pure XML. However, a more practical solution involved TIFF with a metadata encoded jn XML embedded in the headers. Now, and this is the interesting part, a larger consortium (and here is the interesting part) is working on a Next Generation File Format, that does not use HDF5 due to parallel read/write problems, but Zarr. My point being that choosing HDF5 now might has some implications on data access down the road.

> >

> > The more the communities connect the more we can benefit from each other’s previous work.

> >

> > https://ngff.openmicroscopy.org/latest/

> >

> > https://forum.image.sc/tag/ome-ngff

> >

> > https://quarep.org/working-groups/wg-7-metadata/

>

> Thanks - these are strikingly relevant ...

>

> Cheers,

>

> Matthew


The University of Dundee is a registered Scottish Charity, No: SC015096
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