Axondeepseg

[View detailed changelog](https://github.com/neuropoly/axondeepseg/compare/v3.0...v3.2.0)

**BUG**

- Fix redownloading models bug. [View pull request](https://github.com/neuropoly/axondeepseg/pull/322)
- [Bug] Resolve segment folder bug when using relative paths. [View pull request](https://github.com/neuropoly/axondeepseg/pull/320)
- Resolve bug that makes TEM data not segment well (293 and 249). [View pull request](https://github.com/neuropoly/axondeepseg/pull/294)
- Add missing import to apply_model. [View pull request](https://github.com/neuropoly/axondeepseg/pull/290)

**ENHANCEMENT**

- FSLeyes plugin: default morphometrics file extension and font size . [View pull request](https://github.com/neuropoly/axondeepseg/pull/358)
- Remove gaussian blur option for data augmentation. [View pull request](https://github.com/neuropoly/axondeepseg/pull/332)
- Remove overlap when saving masks. [View pull request](https://github.com/neuropoly/axondeepseg/pull/328)
- Resume training from checkpoint. [View pull request](https://github.com/neuropoly/axondeepseg/pull/301)

**FEATURE**

- Add an "Axon numbers" overlay in FSLeyes. [View pull request](https://github.com/neuropoly/axondeepseg/pull/342)
- [FSLeyes plugin] changed Image.save/open with ads_utils.read/write. [View pull request](https://github.com/neuropoly/axondeepseg/pull/296)

**DOCUMENTATION**

- Add warning to doc for re-download of model folders when re-installing. [View pull request](https://github.com/neuropoly/axondeepseg/pull/351)
- Update documentation for manual masks creation. [View pull request](https://github.com/neuropoly/axondeepseg/pull/338)
- Add resampled_resolutions parameter in getting_started notebook. [View pull request](https://github.com/neuropoly/axondeepseg/pull/325)
- [Doc] Add notice about restarting FSLeyes to see the plugin for installation. [View pull request](https://github.com/neuropoly/axondeepseg/pull/317)
- Fix format in Changelog. [View pull request](https://github.com/neuropoly/axondeepseg/pull/291)

**INSTALLATION**

- Fix for the Windows installation. [View pull request](https://github.com/neuropoly/axondeepseg/pull/362)
- Move test images in default models folder. [View pull request](https://github.com/neuropoly/axondeepseg/pull/344)
- Upgrade to Python 3.7. [View pull request](https://github.com/neuropoly/axondeepseg/pull/307)
- Use a specific version of FSLeyes for the plugin. [View pull request](https://github.com/neuropoly/axondeepseg/pull/305)

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**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

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**Changed:**

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

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**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)

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**Changed:**

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

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Versions 1.x will remain Python 2.7-compatible