Deepcell

Bugfixes

* Fix Docker builds by including `README.md` in the Docker image. (462)

| Fraction missed divisions | 0.15 | 0.07 |
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<details>
<summary>Fix bug in calculation of fraction missed divisions msschwartz21 (102)</summary>

Closes 100
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🧰 Maintenance

<details>
<summary>Bump to version 0.6.2 msschwartz21 (104)</summary>


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This release supports TensorFlow 2.3.1+ and drops support for Python 2.7.

Features

* Migrate to TensorFlow 2.3.1 (442)
* `pip install deepcell` is now supported. (461)
* `Applications` load `SavedModels` and are decoupled from the current model architecture. (460)

Bugfixes

* Reduce the number of installed packages in the Dockerfile (442)
* Removed `training.py` from all reference notebooks (458).
* Fixed a `dtype` bug for `disc` transforms (442).

Breaking Changes

* Python 2.7 is no longer supported
* TensorFlow < 2.3.1 is no longer supported.

This will be the final release that supports Python 2.7 and TensorFlow 1.X.

Features

* Visualize RGB data with outlines (441)
* Remove the Resize2D layer. (443)
* Reduce ImageDataGenerator memory footprint. (436)
* Create CellTracking application object, various application bugfixes. (444)
* Use `keras.utils.custom_object_scope` and `keras.testing_utils.layer_test` for testing layers. (447)
* Migrate CI/CD from TravisCI to GitHub Actions. (449, 451, 453)
* Improve docstring RST formatting and include the RTD config file (448)
* Update weights and post-processing parameteres for `deepcell.applications.MultiplexSegmentation`. (434, 452)

Bugfixes

* Do not always save the final model weights in training.py. (435)
* Fix typo in README. (440)
* Add K.epsilon to the denominator in `whole_image` normalization. (446)

🚀 Features

<details>
<summary>Add support for ISBI inputs to the metrics package msschwartz21 (107)</summary>

This addition to the metrics package makes it possible to directly input ISBI style outputs into our metrics pipeline. This simplifies the process of benchmarking against competitor models which tend to output ISBI style tracks.
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🐛 Bug Fixes

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<summary>Implement correct usage of crop parameter in CellTracker msschwartz21 (108)</summary>

- Corrects an error where the crop parameter was not being set during tracking and inference
- Removes deprecated post processing functions from the CellTracker
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🧰 Maintenance

<details>
<summary>REL: pin numpy and update deepcell-toolbox dependency rossbar (110)</summary>

A patch release to upper-bound numpy to prevent errors related to expired scalar deprecations. Bumps the `deepcell-toolbox` dependency as well, which already has more comprehensive fixes for this issue.
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🐛 Bug Fixes

<details>
<summary>Correct keys in `correct_shifted_divisions` msschwartz21 (105)</summary>

Different key names were used in `correct_shifted_divisions` which caused issues in some downstream analyses in the model-registry. This PR standardizes all keys in the metrics package to avoid confusion.
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