Deepcell

Latest version: v0.12.10

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0.8.2

Not secure
Features

* Migrate CI/CD from TravisCI to GitHub Actions (74, 75, 77)

Bugfixes

* Fixed CLAHE normalization bug for negative values (56)

0.8.1

Not secure
Bugfixes

* Pin PyTest<6 to prevent issues with `pytest-pep8` (67)
* Fix the expected multiplex length. (65)
* Handle blank images in `percentile_threshold` preprocessing (69)
* Add epsilon to normalize computation to prevent zero division. (72)

0.8

| Fraction missed divisions | 0.15 | 0.07 |
</details>

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

Closes 100
</details>


🧰 Maintenance

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


</details>

0.8.0

Not secure
Features

* Created `multiplex_utils` for various multiplex formatting, preprocessing, and postprocessing functions.

0.7.0

Features

* Added `percentile_threshold` to clip values above a certain percentile. (60)

Bugfixes

* Fixed issue with Metrics where images with no background would crash. (54)
* Updated Travis tests for python3.5 compatibility. (58)

0.6.5

🐛 Bug Fixes

<details>
<summary>Add epsilon to standard deviation normalization msschwartz21 (119)</summary>


</details>

<details>
<summary>Cast data to correct type in `get_image_features` msschwartz21 (114)</summary>

This PR fixes a bug in `get_image_features`. If the X data is passed in with an integer type (instead of float), the output of `crop_mode='fixed'` and `norm=True` is incorrect. In the examples below, the first image is incorrect while the second is correct.

This PR eliminates the bug by casting X data to float32 and y data to int32 to avoid incorrect use of the function.

<img width="420" alt="Screen Shot 2023-01-24 at 7 34 48 PM" src="https://user-images.githubusercontent.com/20373588/214474471-a4a41fe9-4e58-44a5-8986-2001c0827822.png">
<img width="439" alt="Screen Shot 2023-01-24 at 7 34 38 PM" src="https://user-images.githubusercontent.com/20373588/214474468-1c6ecc00-ec06-4ec6-821b-e5b67b5e9012.png">


</details>


🧰 Maintenance

<details>
<summary>Bump version to 0.6.5 msschwartz21 (120)</summary>


</details>

<details>
<summary>Bump default action versions. rossbar (116)</summary>

Bump action versions to keep CI current, c.f. https://github.com/vanvalenlab/deepcell-tf/pull/653
</details>

<details>
<summary>Reuse indexed array to avoid extra array copies. rossbar (115)</summary>

A minor change that should improve performance. Unfortunately NumPy isn't smart enough to cache indexing results for reuse, so each `app[idx]` invocation of advanced indexing is actually creating a new array (as opposed to a view), resulting in both more memory usage and additional computation time for each allocation. There should be a significant performance boost by only performing the advanced indexing operation once and reusing the result.

Not critically important - just something I noticed while reviewing 114!
</details>

<details>
<summary>Lint with ruff rossbar (113)</summary>

Add the [ruff](https://github.com/charliermarsh/ruff) linter to the development workflow.

Includes basic configuration as well as some minor tweaks/improvements to pass the linter. The configuration is minimal and reflects the original `pytest-pep8` configuration.
</details>

<details>
<summary>Fix failures related to expired usage patterns in dependencies rossbar (112)</summary>

Removes the global warnings filter for deprecation warnings in the test suite and fixes the issues that appear as a result.
</details>

<details>
<summary>Add support for Python 3.10 rossbar (111)</summary>

Cf. vanvalenlab/deepcell-toolbox128
</details>


📚️ Documentation

<details>
<summary>Add references for the AA and TE scores msschwartz21 (118)</summary>


</details>

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