Changelog

Version 3.2.0 - 2020-10-16

View detailed changelog

BUG

Fix redownloading models bug. View pull request
[Bug] Resolve segment folder bug when using relative paths. View pull request
Resolve bug that makes TEM data not segment well (#293 and #249). View pull request
Add missing import to apply_model. View pull request

ENHANCEMENT

FSLeyes plugin: default morphometrics file extension and font size . View pull request
Remove gaussian blur option for data augmentation. View pull request
Remove overlap when saving masks. View pull request
Resume training from checkpoint. View pull request

FEATURE

Add an "Axon numbers" overlay in FSLeyes. View pull request
[FSLeyes plugin] changed Image.save/open with ads_utils.read/write. View pull request

DOCUMENTATION

Add warning to doc for re-download of model folders when re-installing. View pull request
Update documentation for manual masks creation. View pull request
Add resampled_resolutions parameter in getting_started notebook. View pull request
[Doc] Add notice about restarting FSLeyes to see the plugin for installation. View pull request
Fix format in Changelog. View pull request

INSTALLATION

Fix for the Windows installation. View pull request
Move test images in default models folder. View pull request
Upgrade to Python 3.7. View pull request
Use a specific version of FSLeyes for the plugin. View pull request

Version [3.0] - 2020-03-13

Changed:

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.
Shifted AxonDeepSeg from TensorFlow to Keras framework.
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.
Add FSLeyes plugin

Version [2.1] - 2018-09-25

Changed:

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

Version [2.0] - 2018-09-11

Changed:

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)

Version [1.1] - 2018-08-02

Changed:

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

Version [1.0] - 2018-08-02

Versions 1.x will remain Python 2.7-compatible

Version [0.6] - 2018-08-01

(version 0.5 was skipped due to conflicting file on PyPI)

Added:

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

Changed:

Dataset building and training notebook
Minor documentation improvements
Minor bug fixes

Version [0.4.1] - 2018-05-16

Added:

GIMP procedure for ground truth labelling or segmentation correction added in the documentation.
Compatibility with tiff images.
Continuous integration with Travis is now supported.

Changed:

The documentation website is now hosted on ReadTheDocs.
Updated documentation on the usage of AxonDeepSeg.
Change of axon and myelin masks filenames for better clarity.

Version [0.3] - 2018-02-22

Added:

Compatibility for image inputs other than png
Pre-processing of input images is now done inside AxonDeepSeg

Changed:

Help display when running AxonDeepSeg from terminal