axondeepseg - v5.2.0

FEATURE

• Save raw instance segmentation v2 View pull request

BUG

• Quick fix for aggregation file search View pull request

TESTING

• Change mousepress location for tests compatibility with napari>0.6.1 View pull request
• Ensure pip tests only run tests in the latest release branch View pull request

v5.1.1 (2025-07-02)

View detailed changelog

INSTALLATION

• Pin napari<0.6.2 View pull request

- Python
Published by mathieuboudreau 6 months ago

axondeepseg - v5.1.1

View detailed changelog

INSTALLATION

• Pin napari<0.6.2 View pull request

- Python
Published by mathieuboudreau 8 months ago

axondeepseg - v5.1.0

GUI

• Add click to delete "axon" objects and click to view morphometrics View pull request

Installation

• Pre-release changes for 5.1.0 View pull request
• Add checks to run download models if API called without having been downloaded during installation View pull request
• Transition installation from deprecated setup.py+requirements.txt to pyproject.toml View pull request
• Move napari plugin into main package View pull request

CLI

• Log current commit hash in CLI View pull request

Morphometrics

• Morphometric aggregation + visualization View pull request
• Use skimage.measure.label with 1-connectivity View pull request

Testing

• Update skimage and data-testing versions, update morphometrics pkl for consistency check View pull request

BUG

• Create true alias for ads_activate View pull request
• Fix bug loading predictions of grayscale converted img View pull request
• Fix destination feature for download models/tests View pull request
• Make getexistingmodels_list returns None when no models exist View pull request

- Python
Published by mathieuboudreau 8 months ago

axondeepseg - v5.0.1

Bug fix - removed git logging in init.py

- Python
Published by mathieuboudreau about 1 year ago

axondeepseg - v5.0.0

Notable changes include:

• ivadomed to nnunetv2 backend migration. View pull request
• Add napari plugin, set as default GUI tool. View pull request
• Support unmyelinated axons in morphometrics. View pull request
• Add install_ads scripts to automate conda env creation and dependency installation View pull request
• Change "downloadmodels" to "downloadmodel". View pull request
• Remove scikitlearn pinned version and use updated reference pickle for morphometrics data testing View pull request
  • Note: Changes to the latest scikitlearn resulted in slight changes the g-ratio value for some axons. See pull request for more discussion.

Full release notes and Changelog

- Python
Published by mathieuboudreau about 1 year ago

axondeepseg - AxonDeepSeg v4.1.0

Release notes and Changelog

- Python
Published by mathieuboudreau over 3 years ago

axondeepseg - AxonDeepSeg v4.0.0

Release notes and Changelog

- Python
Published by mathieuboudreau about 4 years ago

axondeepseg - AxonDeepSeg v3.3.0

Release notes and Changelog

- Python
Published by mathieuboudreau about 4 years ago

axondeepseg - AxonDeepSeg v3.2.0

Release notes and Changelog

- Python
Published by mariehbourget over 5 years ago

axondeepseg - AxonDeepSeg v3.0

• Add FSLeyes plugin
• Shifted AxonDeepSeg from TensorFlow to Keras framework.
• Refractored data augmentation to use Albumentation library.
• Cleaned jupyter notebooks and reduced from 13 notebooks to 5.
• Switched to Dice Loss from Categorical Cross Entropy as loss function.
• Updated SEM and TEM models for better performance.
• Upgraded CUDA to 10.0 and tensorflow to 1.13.1.
• Resolve image rescale warnings
• Handle exception for images smaller than minimum patch size after resizing
• Revert tensorflow requirekment to 1.3.0 and remove tifffile requirement
• Remove matplotlib.pyplot from source code and refactor to full OO plotting
• Standardize path management to pathlib library
• Shifted AxonDeepSeg from TensorFlow to Keras framework.
• Upgraded CUDA to 10.0 and tensorflow to 1.13.1.

- Python
Published by mathieuboudreau almost 6 years ago

axondeepseg - Release v2.1

– Fixed bug that would crash when user inputed consent for Sentry tracking

- Python
Published by mathieuboudreau over 7 years ago

axondeepseg - Release v2.0

– Upgraded ADS for Python 3.6-compatibility (no longer supporting Python 2.7) – Minor changes to make ADS Windows-compatibile – Removed plot hold commands (deprecated)

- Python
Published by mathieuboudreau over 7 years ago

axondeepseg - Release v1.1

Improvements

– Minor Mac OSX-related bug fix – Changed installation requirements to exact release versions

- Python
Published by mathieuboudreau over 7 years ago

axondeepseg - Release v1.0

Versions 1.x will remain Python 2.7-compatible

- Python
Published by mathieuboudreau over 7 years ago

axondeepseg - Release v0.6

What's new:

• Comprehensive testing suite
• Bug tracking (Sentry)
• Blue-red visualisation function for segmented masks

Improvements:

• Dataset building and training notebook
• Minor documentation improvements
• Minor bug fixes

- Python
Published by mathieuboudreau over 7 years ago

axondeepseg - Release v0.5

(Skipped version due to pre-existence of a v0.5 tagged release on PyPI – refer to v0.6)

- Python
Published by mathieuboudreau over 7 years ago

axondeepseg - Improved usage

• Added possibility to segment all images inside a folder.
• "_segmented" is now added as a suffix to the segmented image (instead of a prefix).
• Added argument -s to specify the acquired resolution of the images to segment.
• Added argument -p to specify the path to the model to use.

- Python
Published by maxwab over 8 years ago

axondeepseg - Release v0.1

This is the first AxonDeepSeg release.

To install it:

pip install AxonDeepSeg-0.1-py2-none-any.whl

Note: Start by creating a Python virtual environment

cd ~
sudo pip install virtualenv
virtualenv ads_venv
source ads_venv/bin/activate

Note: On Yosemite, install tensorflow-1.3.0 prior to AxonDeepSeg:

sudo pip install https://storage.googleapis.com/tensorflow/mac/cpu/tensorflow-1.3.0-py2-none-any.whl

- Python
Published by perone over 8 years ago

axondeepseg -

- Python
Published by vherman3 over 9 years ago