Deepcell-tracking

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

Closes 100
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🧰 Maintenance

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


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🐛 Bug Fixes

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


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<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">


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🧰 Maintenance

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


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

Cf. vanvalenlab/deepcell-toolbox128
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📚️ Documentation

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


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🚀 Features

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<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

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<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

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<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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🐛 Bug Fixes

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<summary>Classify divisions that are +/- 1 frame as correct msschwartz21 (103)</summary>

Recent reviews of tracking predictions have identified a failure mode in the current metrics packages. Different segmentation predictions can sometimes lead to a cell dividing in one frame before or after the frame assigned to the division in the ground truth. Currently this leads to that division counting as both a false positive and a missed division. This PR introduces a new metrics function that identifies these events and corrects the metrics to classify this division as correct. Additionally a new metrics class for tracking (`TrackingMetrics`) has been introduced to coordinate running all of the necessary metrics functions.

In the current test split, applying the new metrics pipeline led to the following changes in metrics:
| Metric | Old | New |
|-------------------------------|------|------|
| Total divisions | 181 | 181 |
| Correct divisions | 139 | 154 |
| False negative division | 27 | 13 |
| False positive division | 40 | 26 |
| Mismatch division | 15 | 14 |
| Division Recall | 0.84 | 0.92 |
| Division Precision | 0.78 | 0.86 |
| Division F1 | 0.81 | 0.89 |

🧰 Maintenance

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<summary>Bump to 0.6.1 msschwartz21 (99)</summary>


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<summary>Enable option for fixed size crops in get_image_features vanvalen (98)</summary>

What
Add a flag to get_image_features to allow for doing fixed sized crops rather than crop and resize.

Why
Crop and resize removes information about cell size, which is useful for cell tracking and also learning dynamic representations of cell behavior.
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