[scikit-learn] ANN: DIPY 1.1.1 - a powerful release

Wed Jan 22 10:54:04 EST 2020

Hello Joel,

Here is the short description about DIPY as requested.

DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic
methods for spatial normalization, signal processing, machine learning,
statistical analysis and visualization of medical images. Additionally, it
contains specialized methods for computational anatomy including
diffusion, perfusion and structural imaging.

Gael and Alex from sklearn's leadership team are aware of the project and
its importance to the Pythonic community.
Have in mind that there is an extremely low number of community based open
source projects in medical imaging in Python
and DIPY is one of the very few examples that is actually stable and
growing. DIPY is quite unique because it provides methods
(algorithms developed from scratch in Python) for solving medical imaging
problems. Some of the algorithms are very generic
for example we have image registration and denoising algorithms and can be
used across fields. It is true that in our website it
shows that focus is on diffusion imaging but now this is changing and we
will be updating all our websites and systems
accordingly to explain the more generic extent of the library during the
following weeks.

Your call at the end. It would be nice if you can spread the word. No hard
feelings otherwise.

Best,
Eleftherios

On Sat, Jan 18, 2020 at 8:12 AM Joel Nothman <joel.nothman at gmail.com> wrote:

> If the Scikit-learn mailing list is going to include announcements of
> related package releases, could we please get a line or two describing that
> package? I expect most readers here don't know of DIPY, or of its relevance
> to Scikit-learn users. (I'm still not sure why it's generally relevant to
> scikit-learn users.)
>
> Thanks
>
> On Fri, 17 Jan 2020 at 04:04, Eleftherios Garyfallidis <
> garyfallidis at gmail.com> wrote:
>
>> We are excited to announce a new release of DIPY:
>>
>>
>> DIPY 1.1.1 is out! In addition:
>>
>>
>> a) A new 5 day workshop available during March 16-20 to learn the theory
>> and applications of the hundreds of methods available in DIPY 1.1.1
>> Intense!
>>
>> See the exquisite program here <https://workshop.dipy.org>.
>>
>> *b) Given the need for a myriad of new DIPY derivative projects, DIPY
>> moved to its own organization in GitHub. **Long live DIPY! *
>> *And therefore, *https://github.com/dipy/dipy* supersedes https://github.com/nipy/dipy
>> <https://github.com/nipy/dipy> The old link will be available as a redirect
>> link for the next 6 months.*
>>
>> c) Please support us by *citing** DIPY* in your papers using the
>> following DOI: 10.3389/fninf.2014.00008
>> <https://www.ncbi.nlm.nih.gov/pubmed/24600385>otherwise the DIPY
>> citation police will find you. ;)
>>
>> DIPY 1.1.1 (Friday, 10 January 2020)
>>
>> This release received contributions from 11 developers (the full release
>> notes are at:
>> https://dipy.org/documentation/1.1.1./release_notes/release1.1/). Thank
>> you all for your contributions and feedback!
>>
>> Please click here <https://dipy.org/documentation/1.1.1./api_changes/>
>> to check API changes.
>>
>> Highlights of this release include:
>>
>>    -
>>
>>    New module for deep learning DIPY.NN (uses TensorFlow 2.0).
>>    -
>>
>>    Improved DKI performance and increased utilities.
>>    -
>>
>>    Non-linear and RESTORE fits from DTI compatible now with DKI.
>>    -
>>
>>    Numerical solutions for estimating axial, radial and mean kurtosis.
>>    -
>>
>>    Added Kurtosis Fractional Anisotropy by Glenn et al. 2015.
>>    -
>>
>>    Added Mean Kurtosis Tensor by Hansen et al. 2013.
>>    -
>>
>>    Nibabel minimum version is 3.0.0.
>>    -
>>
>>    Azure CI added and Appveyor CI removed.
>>    -
>>
>>    New command line interfaces for LPCA, MPPCA and Gibbs Unringing.
>>    -
>>
>>    New MTMS CSD tutorial added.
>>    -
>>
>>    Horizon refactored and updated to support StatefulTractograms.
>>    -
>>
>>    Speeded up all cython modules by using a smarter configuration
>>    setting.
>>    -
>>
>>    All tutorials updated to API changes and 2 new tutorials added.
>>    -
>>
>>    Large documentation update.
>>    -
>>
>>    Closed 126 issues and merged 50 pull requests.
>>
>> Note:
>>
>>    -
>>
>>    Have in mind that DIPY stopped supporting Python 2 after version
>>    0.16.0. All major Python projects have switched to Python 3. It is time
>>    that you switch too.
>>
>>
>>
>> To upgrade or install <http://dipy.org/release0.10.html> DIPY
>>
>> Run the following command in your terminal:
>> <http://dipy.org/release0.10.html>
>>
>> pip install --upgrade dipy
>>
>> or
>>
>> conda install -c conda-forge dipy
>>
>> This version of DIPY depends on nibabel (3.0.0+).
>>
>> For visualization you need FURY (0.4.0+).
>>
>> Questions or suggestions?
>>
>>
>>
>> For any questions go to http://dipy.org, or send an e-mail to
>> dipy at python.org <neuroimaging at python.org>
>>
>> We also have an instant messaging service and chat room available at
>> https://gitter.im/nipy/dipy
>>
>> On behalf of the DIPY developers,
>>
>> Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro
>>
>> https://dipy.org/contributors
>>
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