[Neuroimaging] CZI grant - what would you like to see in Nibabel?

[Steve Pieper]

Hi Mathew and all -

These are all great ideas.  +100 for better python imaging tools!

Regarding tractography data formats you may be interested in leveraging the
new trako format.  Preprint and pypi link below.  It leverages glTF/draco
compression and has nice features to trade off file size for lossiness and
also compresses extra data fields.

https://arxiv.org/pdf/2004.13630.pdf

https://pypi.org/project/trako/

Cheers,
Steve



On Thu, Jul 30, 2020 at 12:15 PM Matthew Brett <matthew.brett at gmail.com>
wrote:

> Hi,
>
> Emanuele - would you mind opening an issue for this?
>
> Can anyone volunteer to lead the new streamlines format group?  I'm
> not an expert at all.
>
> Cheers,
>
> Matthew
>
> On Thu, Jul 30, 2020 at 5:03 PM Emanuele Olivetti <olivetti at fbk.eu> wrote:
> >
> > Hi Matthew,
> >
> > My colleagues and I would like to have a (much) faster loader of
> tractography data with a smaller memory footprint, especially for TRK
> (Trackvis) files. Just to give you an idea - which, yes, it's an extreme
> case but definitely not so infrequent for us - when loading a very large
> tractogram of 10 million streamlines it takes:
> > - 15 minutes and approximately 10Gb of RAM with Nibabel
> > - 1 minute and approximately 5Gb of RAM with our custom TRK loader (it
> works but code style is meh,
> https://github.com/FBK-NILab/nilab/blob/master/load_trk.py)
> > - 6 seconds and 3.5Gb of RAM if we previously save the tractogram as
> numpy array (numpy.savez()) and then load it with numpy.load(). But in this
> case, the streamlines are resampled to a fixed number of points.
> >
> > Thank you for all the work done!
> >
> > Emanuele
> >
> >
> > On Thu, Jul 30, 2020 at 5:01 PM Matthew Brett <matthew.brett at gmail.com>
> wrote:
> >>
> >> Hi,
> >>
> >> Although this is pushing things close the wire, I am currently trying
> >> to work out whether to apply for a Chan Zuckerberg grant for Nibabel:
> >>
> >>
> https://chanzuckerberg.com/wp-content/uploads/2020/06/EOSS-3-RFA-Announcement-and-Instructions-CYCLE-3-COMBINED-1.pdf
> >>
> >> Before we do that, I wanted to ask - if y'all could get anything into
> >> Nibabel - what
> >> would it be?
> >>
> >> So far, in various conversations, Chris Markiewicz and I came up with:
> >>
> >> * More comprehensive DICOM to NIfTI etc support
> >> * Labelled axes for images, maybe via xarray
> >> * Integrated API for surface formats [1]
> >> * HDF5 serialization for many image formats
> >> * Ability to read images directly from URLs, read / write images to /
> >> from AWS, GCS, Azure data storage addresses [2]
> >> * Optimized visualization for web and desktop
> >>
> >> Is there anything else you'd like to see?
> >>
> >> See you,
> >>
> >> Matthew
> >>
> >> [1] https://github.com/nipy/nibabel/issues/936
> >> [2] c.f.
> https://pandas.pydata.org/pandas-docs/version/1.1.0/whatsnew/v1.1.0.html#fsspec-now-used-for-filesystem-handling
> >> _______________________________________________
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> >
> >
> >
> > --
> > Emanuele Olivetti, Ph.D.
> > Senior Research Scientist at Bruno Kessler Foundation (FBK-ICT)
> > NeuroInformatics Laboratory (NILab) http://nilab.fbk.eu
> > Center for Mind and Brain Sciences (CIMeC), University of Trento
> > Via delle Regole 101 - 38123 Mattarello (Trento), ITALY
> > olivetti at fbk.eu - +39 0461314179
> > emanuele.olivetti at unitn.it - +39 0461282760
> >
> >
> >
> > FBK vi invita a leggere il suo Piano di rientro | FBK invites you to
> read its Premises Reopening Plan.
> >
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