[Neuroimaging] Planning for data formats - upcoming journal club

Nate Vack njvack at wisc.edu
Tue Nov 9 09:31:11 EST 2021

Hey there,

Thanks for putting the thought into this! Having used HDF5 myself a bit, I
tend to agree that it's a bit awkward in practice. Machine-readable-only
metadata is not great and the installation process is usually fine, except
when it... isn't.

Looking at the ASDF spec, it does seem pretty compelling.

I probably don't have a deep enough background in this to add much to your
discussion, but I'm super interested to see where this goes. I will be very
happy to live in a world without .json sidecars :)

Best regards!

On Tue, Nov 9, 2021 at 7:48 AM <andersonwinkler at gmail.com> wrote:

> Hi Matthew, hi all,
> I put some thinking on this a few years ago and concluded that HDF5 would
> be ideal. The blog post you link was already up and I didn't feel deterred
> by it, despite the interesting insights.
> At the time I put online a document for discussion (
> https://docs.google.com/document/d/1s5DX4YPS680mc3Rb9msLetrjlPcDhaw835Um-jJb-Dw/edit?usp=sharing)
> and as a starting point, made a mapping to how we'd store NIFTI as HDF5 (
> https://docs.google.com/document/d/1hL27J2wNqHj27aX3VrCY8ajHyIBYtgYVmNmSoZZC8aA/edit?usp=sharing
> ).
> At the end, I had to focus on other things, including career (and country)
> moves, and couldn't spend time and effort on this, despite the fact that
> the needs from then continue very much the same as today (if not perhaps
> even more needed now than then...).
> I'd be happy to participate in any effort you or others may lead towards
> this.
> Cheers,
> Anderson
> On Tue, Nov 9, 2021 at 8:24 AM KEVEEN RODRIGUEZ ZAPATA <
> keveen.rodriguez at udea.edu.co> wrote:
>> Hello, thanks for the initiative Matthew, I would like to be part of the
>> schedule.
>> On Tue, 9 Nov 2021 at 6:32 AM Matthew Brett <matthew.brett at gmail.com>
>> wrote:
>>> Hi,
>>> Summary:  we are planning to do a journal club to discuss new
>>> neuroimaging data formats.  Please let me (Matthew) know if you want
>>> to be included in the scheduling for the journal club.  Of course,
>>> once we've got a time, anyone can join the journal club Zoom.
>>> Detail:
>>> As part of the Chan-Zuckerberg grant work, we are thinking about new
>>> formats for using and sharing neuroimaging data.
>>> As you can see in the grant documents:
>>> https://github.com/matthew-brett/czi-nibabel
>>> we've been thinking about HDF5, but further research (e.g. [1]) has
>>> given us some pause for reflection.  Meanwhile, the astronomy
>>> community has done some serious thinking about this, and written this
>>> up in a paper proposing a new astronomy format:
>>> Greenfield, M. Droettboom, E. Bray,
>>> ASDF: A new data format for astronomy,
>>> Astronomy and Computing,
>>> Volume 12,
>>> 2015,
>>> Pages 240-251,
>>> ISSN 2213-1337,
>>> https://doi.org/10.1016/j.ascom.2015.06.004.
>>> (https://www.sciencedirect.com/science/article/pii/S2213133715000645)
>>> Both the discussion and the format seem like a very good starting
>>> point for our own thinking about data formats, so we'd like to have a
>>> journal club to discuss it.
>>> I (Matthew) am going to organize this via Calendly, and I've made a
>>> Caldendly account for Nipy-related stuff, but, if you want to have a
>>> say in when we do the journal club, please let me know so I can add
>>> you to that account.  I'll publish the Calendly link in a day or so.
>>> Cheers,
>>> Matthew
>>> [1] https://cyrille.rossant.net/moving-away-hdf5/
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>> --
>> Keveen Rodríguez Zapata
>> B.Eng. Bioengineer
>> Msc. Student in Biomedical Sciences: Neuroscience and Bsc. Computer
>> Science
>> Universidad de Antioquia
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