Changelog
v4.1.0 (2022-10-07)
BUG
Resolve “tif in filename” imread bug & refactor valid image exensions. View pull request
Fix morphometrics bug when writing index/axonmyelin_index files. View pull request
ENHANCEMENT
--border-info
option for morphometrics (optical fractionator technique). View pull requestAdd border_touching flag to morphometrics. View pull request
Zoom factor sweep. View pull request
Zoom factor option for segmentation via CLI. View pull request
FEATURE
Save instance segmentation image. View pull request
Add logging for segmentation/morphometrics. View pull request
Zoom factor sweep. View pull request
DOCUMENTATION
Add model repo links in the doc. View pull request
INSTALLATION
Simplify specifying torch dependency. View pull request
Update ivadomed to 2.9.5. View pull request
Update ivadomed to 2.9.4. View pull request
TESTING
Add test for 16bit TIF grayscale file. View pull request
environment.yaml
: Pinpillow!=9.0.0
. View pull request
Version 4.0.0 - 2022-02-03
NOTICE
Due to the change in implementations on an upgraded dependency (skimage v0.14.2 -> v0.18.3), the morphometrics values “solidity” and “orientation” differ from values produced by AxonDeepSeg v3.x. “solidity” values produced can vary slightly due to numerical precision in algorithmic changes in skimage (on the order of 1%), a the convention for “orientation” changed from “rc” to “xy”, leading to a difference in value by pi/2. See this issue for more details: https://github.com/neuropoly/axondeepseg/issues/589
BUG
Fix NaNs not appearing when generating morphometrics with the GUI View pull request
FEATURE
Integrate IVADOMED into project View pull request
Changed all instances of imageio_imread by ads_utils.imread View pull request
INSTALLATION
Added Mac M1 compatibility View pull request
Version 3.3.0 - 2022-01-14
BUG
Fix morphometrics error with ellipse axon shape View pull request
Fix patches2im_overlap when width = height View pull request
Patch myelin thickness calculation View pull request
Bug fix due to h5py package version in fsleyes View pull request
Pin h5py~=2.10.0 as a workaround for upstream Keras/TensorFlow issues View pull request
Resolve bug that makes TEM data not segment well with multiple files View pull request
ENHANCEMENT
Added the axon shape selection in the GUI (take two) View pull request
Generate numbers image with CLI View pull request
Refactor the code for the settings menu View pull request
Add Optical Microscopy model in notebooks View pull request
Add perimeter to morphometricsView pull request
Add CLI support to generate morphometrics file. View pull request
Replaced rcParams with font_manager to find the font View pull request
Remove wildcard imports View pull request
Migration to GitHub Actions View pull request
Change the name of -o flag to -overlap flag View pull request
Add a model to .gitignore View pull request
Change the default name for saving the morphometrics file View pull request
Use pathlib in the ads_plugin instead of os.path View pull request
Integrate Simeon’s model with FSLeyes and CLI View pull request
Fix Naming Convention View pull request
Fixed Notebooks and Binder links in docView pull request
Move test files to OSF, add download functionality View pull request
Add postprocessing tests View pull request
FEATURE
Implement Batch morphometrics for images present in directory/directories View pull request
Implement Ellipse Minor Axis as Diameter View pull request
Add a settings menu to the FSLeyes plugin View pull request
Add Axon mask simulator View pull request
DOCUMENTATION
Update Youtube video links View pull request
Apply RTD fix to make builds pass again View pull request
Update figure link View pull request
Migrate images to new repo View pull request
Change link View pull request
Add description of morphometrics columns headings View pull request
Add a reference to Readme.md View pull request
Update the documentation for installing the GPU compatible version of ADS View pull request
Add tutorial video link in RTD View pull request
Fix docs for optical microscopy model View pull request
Documentation updates View pull request
Fix new changelog display in RTD View pull request
Add zoomed window on masks examples in RTD View pull request
Remove PyPI install instructions from RTD View pull request
Fix youtube video link in RTD View pull request
INSTALLATION
Link the test_files to GitHub View pull request
Download models from Github repo View pull request
Generate images synthetically in tests View pull request
Change install to one env file & update docs View pull request
Refactor AxonDeepSeg/models directory and update .gitignore View pull request
Change how ADS dependencies are installed View pull request
Add PR template View pull request
Remove old config file (set_config) View pull request
Version 3.2.0 - 2020-10-16
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
fromCategorical 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 plottingStandardize path management to
pathlib
libraryShifted 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