<div dir="ltr"><div>hi,</div><div><br></div>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.<div><br></div><div><div>while interested in attending, i would suggest scheduling without me, and will join if i can or comment on a doc as necessary.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">cheers,<br><br>satra</div></div></div></div></div></div></div></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Nov 9, 2021 at 9:16 AM JB Poline <<a href="mailto:jbpoline@gmail.com">jbpoline@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi, <br></div><div><br></div><div>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</div><div><br></div><div>I'd be interested as well <br></div><div>Cheers</div><div>JB<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Nov 9, 2021 at 8:48 AM Anderson M. Winkler <<a href="mailto:andersonwinkler@gmail.com" target="_blank">andersonwinkler@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Matthew, hi all,<div><br></div><div>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.</div><div><br></div><div>At the time I put online a document for discussion (<a href="https://docs.google.com/document/d/1s5DX4YPS680mc3Rb9msLetrjlPcDhaw835Um-jJb-Dw/edit?usp=sharing" target="_blank">https://docs.google.com/document/d/1s5DX4YPS680mc3Rb9msLetrjlPcDhaw835Um-jJb-Dw/edit?usp=sharing</a>) and as a starting point, made a mapping to how we'd store NIFTI as HDF5 (<a href="https://docs.google.com/document/d/1hL27J2wNqHj27aX3VrCY8ajHyIBYtgYVmNmSoZZC8aA/edit?usp=sharing" target="_blank">https://docs.google.com/document/d/1hL27J2wNqHj27aX3VrCY8ajHyIBYtgYVmNmSoZZC8aA/edit?usp=sharing</a>).</div><div><br></div><div>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...).</div><div><br></div><div>I'd be happy to participate in any effort you or others may lead towards this.</div><div><br></div><div>Cheers,</div><div><br></div><div>Anderson</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Nov 9, 2021 at 8:24 AM KEVEEN RODRIGUEZ ZAPATA <<a href="mailto:keveen.rodriguez@udea.edu.co" target="_blank">keveen.rodriguez@udea.edu.co</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="auto">Hello, thanks for the initiative Matthew, I would like to be part of the schedule.<br></div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 9 Nov 2021 at 6:32 AM Matthew Brett <<a href="mailto:matthew.brett@gmail.com" target="_blank">matthew.brett@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi,<br>
<br>
Summary:Â we are planning to do a journal club to discuss new<br>
neuroimaging data formats. Please let me (Matthew) know if you want<br>
to be included in the scheduling for the journal club. Of course,<br>
once we've got a time, anyone can join the journal club Zoom.<br>
<br>
Detail:<br>
<br>
As part of the Chan-Zuckerberg grant work, we are thinking about new<br>
formats for using and sharing neuroimaging data.<br>
<br>
As you can see in the grant documents:<br>
<br>
<a href="https://github.com/matthew-brett/czi-nibabel" rel="noreferrer" target="_blank">https://github.com/matthew-brett/czi-nibabel</a><br>
<br>
we've been thinking about HDF5, but further research (e.g. [1]) has<br>
given us some pause for reflection. Meanwhile, the astronomy<br>
community has done some serious thinking about this, and written this<br>
up in a paper proposing a new astronomy format:<br>
<br>
Greenfield, M. Droettboom, E. Bray,<br>
ASDF: A new data format for astronomy,<br>
Astronomy and Computing,<br>
Volume 12,<br>
2015,<br>
Pages 240-251,<br>
ISSN 2213-1337,<br>
<a href="https://doi.org/10.1016/j.ascom.2015.06.004" rel="noreferrer" target="_blank">https://doi.org/10.1016/j.ascom.2015.06.004</a>.<br>
(<a href="https://www.sciencedirect.com/science/article/pii/S2213133715000645" rel="noreferrer" target="_blank">https://www.sciencedirect.com/science/article/pii/S2213133715000645</a>)<br>
<br>
Both the discussion and the format seem like a very good starting<br>
point for our own thinking about data formats, so we'd like to have a<br>
journal club to discuss it.<br>
<br>
I (Matthew) am going to organize this via Calendly, and I've made a<br>
Caldendly account for Nipy-related stuff, but, if you want to have a<br>
say in when we do the journal club, please let me know so I can add<br>
you to that account. I'll publish the Calendly link in a day or so.<br>
<br>
Cheers,<br>
<br>
Matthew<br>
<br>
[1] <a href="https://cyrille.rossant.net/moving-away-hdf5/" rel="noreferrer" target="_blank">https://cyrille.rossant.net/moving-away-hdf5/</a><br>
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</blockquote></div></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font size="2"><br></font></div><div><font size="2" face="monospace, monospace" color="#444444">Keveen RodrÃguez Zapata</font></div><div><font size="2" face="monospace, monospace" color="#444444">B.Eng. Bioengineer</font></div><div><font size="2" face="monospace, monospace" color="#444444">Msc. Student in Biomedical Sciences: Neuroscience and Bsc. Computer Science</font></div><div><span style="color:rgb(68,68,68);font-family:monospace,monospace">GRUNECO</span><font size="2" face="monospace, monospace" color="#444444"><br></font></div><div><font size="2"><font face="monospace, monospace" color="#444444">Universidad de Antioquia<br></font><br></font></div><div dir="ltr"><font size="2"><a href="http://www.biomaterialesudea.com.co" target="_blank"></a></font></div></div></div></div></div></div></div></div></div></div></div></div></div>
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