Deepcell

This release fully supports Tensorflow 1.10.x through 1.14.x, and Python 2.7, 3.5, 3.6. Future releases will drop support for TensorFlow 1.10.x, 1.11.x 1.12.x, 1.13.x as well as dropped support for Python 3.5.

Features

* Replaces `tracking.py` and `tracking_utils.py` with a dependency on the pip package `deepcell_tracking`. (PR 254)

* Break `image_generators.py` into a submodule with each family of generators in a different file. (PR 258)

Bugfixes

* Updated `reshape_matrix` to work with non-square matrices. (PR 257)

* Fixed namespace imports. (PR 262)

* 3D FeatureNet models can now be re-instantiated with a new frames_per_batch value. (PR 250)

Breaking Changes

* Updates the `ImageNormalization` layers to not have trainable weights (PR 250), which unfortunately means that models trained in versions <0.4.0 cannot be loaded with version 0.4.0+.

Known Issues

* While this release supports TensorFlow 1.12.x and 1.13.x, there have been compatibility issues with these versions in the past (244 and 245).

Bugfixes

* Updated copyright year to 2021 (38)
* Manually delete `tempfile.NamedTemporaryFiles` to resolve bug on Windows (40, 41)
* Avoid integer overflow in `clean_up_annotations` (42)

Dependencies

* Use environment markers to conditionally install compatible versions of `opencv-python-headless` based on Python version (39)
* Change pinned `scikit-image` version from < 17 to >= 0.14.5 (48)

frames_per_batch` was added to both `RetinaNet` and `RetinaMask` which have both been adapted for 3D data if `frames_per_batch` is greater than 1.

Other bugs were fixed:
* Issue 225 was resolved, enabling compatibility testing with TensorFlow 1.14.0.
* Issue 219 was also resolved and tests were improved to ensure sequential labels for reshaped data.
* Tests for `deepcell.model_zoo` and `deepcell.applications` were also significantly improved by parameterizing tests instead of using a for-loop.

Features

* Migrate CI/CD from TravisCI to GitHub Actions. (32)
* Replaced `opencv-python` with `opencv-python-headless` for faster builds and fewer dependencies. (33)

Bugfixes

- Pin OpenCV <= 3.4.9.31 for wider Python support. (31)

The 0.2.5 release makes a few small code improvements such as:

* Adding an inner function `_track_frame` to be called in the frame loop inside `track_cells`.

* Improving the consistency of method/class names across all files.

* Adds tests for the I/O utility functions, and improves code coverage to >80%.