ANN: DIPY 1.8.0

2023-12-23 Thread Eleftherios Garyfallidis via Python-list 
Hello all,

We are excited to announce a new release of DIPY: DIPY 1.8.0 ! This release
includes many new features and updates to support the latest Python, Numpy,
Scipy and Cython versions. The Pythonic ecosystem is growing fast. Which is
great. But please report any issues you may find.

DIPY 1.8.0 (Friday, 13 December 2023)

The release 1.8.0 received contributions from 28 developers (the full
release notes are at:
https://docs.dipy.org/stable/release_notes/release1.8.html).

Thank you all for your contributions and feedback!

Please click here
 to check
1.8.0 API changes.

Highlights of 1.8.0 release include:


   -

   Python 3.12.0 support.
   -

   Cython 3.0.0 compatibility.
   -

   Migrated to Meson build system. Setuptools is no more.
   -

   EVAC+ novel DL-based brain extraction method added.
   -

   Parallel Transport Tractography (PTT) 10X faster.
   -

   Many Horizon updates. Fast overlays of many images.
   -

   New Correlation Tensor Imaging (CTI) method added.
   -

   Improved warnings for optional dependencies.
   -

   Large documentation update. New theme/design integration.
   -

   Closed 197 issues and merged 130 pull requests.

Here is also a reminder of the previous highlights (which was not announced
- due to the large changes in the Pythonic ecosystem).

Highlights of 1.7.0 release include:


   -

   NF: BundleWarp - Streamline-based nonlinear registration method for
   bundles added.
   -

   NF: DKI+ - Diffusion Kurtosis modeling with advanced constraints added.
   -

   NF: Synb0 - Synthetic b0 creation added using deep learning added.
   -

   NF: New Parallel Transport Tractography (PTT) added.
   -

   NF: Fast Streamline Search algorithm added.
   -

   NF: New denoising methods based on 1D CNN added.
   -

   Handle Asymmetric Spherical Functions.
   -

   Large update of DIPY Horizon features.
   -

   Multiple Workflows updated
   -

   Large codebase cleaning.
   -

   Large documentation update. Integration of Sphinx-Gallery.
   -

   Closed 53 issues and merged 34 pull requests.

To upgrade or install  DIPY

Run the following command in your terminal (works across Mac, Linux, Win):


pip install --upgrade dipy

This version of DIPY depends on nibabel (3.0.0+).

For visualization you need FURY (0.9.0+).

Questions or suggestions?



For any questions go to our new website at https://dipy.org, or send an
e-mail to d...@python.org

We also have an instant messaging service and chat room available at
https://gitter.im/dipy/dipy

Finally, a new discussion forum is available at
https://github.com/dipy/dipy/discussions

Have a wonderful time using this new version and please support us by citing
DIPY in your papers using the following DOI: 10.3389/fninf.2014.8



In addition, registration for the online DIPY workshop 2024 (March 11-15)
is open! The workshop will continue equipping you with the skills and
knowledge needed to master the latest techniques and tools in structural
and diffusion imaging. See the exquisite program and keynote speakers here
.

Register now !


On behalf of the DIPY developers,

Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro

https://dipy.org/contributors
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ANN: Happy 2025 with DIPY 1.10.0 💥

2025-01-07 Thread Eleftherios Garyfallidis via Python-list 
Hello and Happy 2025 to all !,

We are excited to announce a new release of DIPY: DIPY 1.10.0 !

DIPY 1.10.0 (Friday, 12 December 2024)

The release 1.10.0 received contributions from 28 developers (the full
release notes are at:
https://docs.dipy.org/stable/release_notes/release1.10.html).

Thank you all for your contributions and feedback!

Please click here
 to
check 1.10.0 API changes.

Highlights of 1.10.0 release include:

- NF: Patch2Self3 - Memory less denoising for dMRI is now available.

- NF: Fiber density and spread from ODF using Bingham distributions method
added.

- NF: Iteratively reweighted least squares for robust fitting of diffusion
models added.

- NF: NDC - Neighboring DWI Correlation quality metric added.

- NF: DAM - DWI-based tissue classification method added.

- NF: New Parallel Backends (Ray, Joblib, Dask) for fitting reconstruction
methods added.

- RF: Deprecation of Tensorflow support. PyTorch support is now the default.

- Transition to Keyword-only arguments (PEP 3102).

- Zero-warnings policy (CIs, Compilation, doc generation) adopted.

- Adoption of ruff for automatic style enforcement.

- Transition to using f-strings.

- Citation system updated. It is more uniform and robust.

- Multiple Workflows updated.

- Multiple DIPY Horizon features updated.

- Large documentation update.

- Closed 258 issues and merged 187 pull requests.


To upgrade or install  DIPY

Run the following command in your terminal:


pip install --upgrade dipy

This version of DIPY depends on nibabel (3.0.0+).

For visualization you need FURY (0.12.0+).

Questions or suggestions?



For any questions go to https://dipy.org, or send an e-mail to
d...@python.org

We also have an instant messaging service and chat room available at
https://gitter.im/dipy/dipy

Finally, a new forum is available at
https://github.com/dipy/dipy/discussions

Have a wonderful time using the new version.

In addition, registration for the online DIPY workshop 2025 (March 17-21)
is open! The workshop will equip you with the skills and knowledge needed
to master the latest techniques and tools in structural and diffusion
imaging. See the exquisite program and keynote speakers here
. Register today to save a spot!

Please support us by citing DIPY in your papers using the following
DOI: 10.3389/fninf.2014.8



On behalf of the DIPY developers,

Eleftherios Garyfallidis, Ariel Rokem, Serge Koudoro

https://dipy.org/contributors
-- 
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Join us for the 2025 DIPY Workshop! - March 17-21 Online! - Early Bird Ends Jan 3rd!

2024-12-17 Thread Eleftherios Garyfallidis via Python-list 
Dear All,

DIPY is a software that analyzes structural and diffusion MRI images using
Python. We are excited to invite you to our upcoming DIPY workshop, which
will take place from March 17 to March 21, 2025. This year, we promise an
enriching experience as we dive into the world of AI in advanced imaging
and data analytics.

Our distinguished keynote speakers include Prof. Simon Warfield (Harvard
Medical School), Prof. Alexandra Badea (Duke University), Prof. Franco
Pestilli (University of Texas at Austin), Prof. Marco Palombo (Cardiff
University), and Prof. Julien Cohen-Adad (Polytechnique Montreal).

Additionally, Koudoro, Descoteaux, Tang, Rokem, Chandio, Fadnavis,
Henriques, Legarreta, and others will present various techniques in medical
imaging, including (but not limited to) pre-processing, reconstruction,
denoising, microstructure modeling, tractography, and visualization.

This year’s highlights include the overview of our *new ultra-fast tracking*
API by Girard (CPU) and Kruper (GPU) and much more!

The DIPY workshop aims to train the next generation of scientists, doctors,
and engineers who will shape the future of medical imaging. Your
participation will contribute greatly to the success of this event.

As is customary for the DIPY workshop, the following will be available:

   -

   Daily hands-on sessions for guided practice
   -

   Opportunities for attendees to present their work or problems of interest
   -

   Certificates of Attendance

Please visit our website *here*
 to register for
the workshop. We look forward to your participation and to exploring the
exciting work of imaging science together.

DIPY is also offering Early Bird discounts until January 3rd, 2025.
Register soon to take advantage of these offers!

For any concerns, please email *works...@dipy.org *.
On behalf of the DIPY team,
Eleftherios Garyfallidis, PhD
DIPY Founder & Lead
Associate Professor
Intelligent Systems Engineering
Indiana University
Luddy Hall 700 N Woodlawn
Bloomington, IN 47408
GRG  | DIPY  | FURY

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