[Neuroimaging] Planning for data formats - upcoming journal club

Tue Nov 9 09:32:24 EST 2021

hi,

i can help provide a data archiving, metadata, and cloud/hpc access
perspective. we are using hdf5 quite a bit both through nwb and otherwise
at present, and are also using zarr, a cloud native format. i would not
write off hdf5 and instead ask which use cases in what physical
environments would run you into trouble.

while interested in attending, i would suggest scheduling without me, and
will join if i can or comment on a doc as necessary.

cheers,

satra

On Tue, Nov 9, 2021 at 9:16 AM JB Poline <jbpoline at gmail.com> wrote:

> Hi,
>
> Another thing that could be useful would be to have a look at the NWB
> folks experience - they have gone through quite a few pain points - we ask
> one of the developer to give a little talk / summary of their experience
>
> I'd be interested as well
> Cheers
> JB
>
> On Tue, Nov 9, 2021 at 8:48 AM Anderson M. Winkler <
> 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/
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>>> --
>>>
>>> Keveen Rodríguez Zapata
>>> B.Eng. Bioengineer
>>> Msc. Student in Biomedical Sciences: Neuroscience and Bsc. Computer
>>> Science
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