0.4.1

🧰 Maintenance

Bump deepcell-toolbox to 0.10.x @willgraf (#60)

This PR bumps the deepcell-toolbox dependency to 0.10.0.

0.4.0

🚀 Features

Update Tracking Approach and Address Outstanding Bugs @MekWarrior (#53)

What

• End-to-End updates for DeepCell's approach to the tracking problem in live-cell imaging. A new Track object is introduced to hold track information and allow for augmentation using the new dataset builder module in deepcell-tf. This PR introduces breaking changes related to the previous LSTM and Siamese Neural Network (SNN) model architecture. The updated CellTracker object is intended for use with the inference model and neighborhood encoders generated and trained by the new graph-based tracking architecture in deepcell-tf. Additionally, the utils related to benchmarking have been updated and improved.

Why

• These updates represent the natural evolution of the repo's approach to tracking. It addresses key needs to further enable adoption of TF2 and dramatically improves tracking speed. At the same time, it address several bugs that have been uncovered since deepcell-tracking was first introduced.

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This PR should also fix several old issues:

• Fixes #13 (Removes compute_distance)
• Fixes #14 (Prefetches all cell features, no repeated loops)
• Fixes #35 (removes _get_input_pairs)

🧰 Maintenance

Fix PyPI version badge URL. @willgraf (#49)

Update version to 0.4.0 @willgraf (#58)

Create release-drafter workflow to draft releases automatically. @willgraf (#59)

0.3.1

0.3.1

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)

0.3.0

0.3.0

Features

• Updated tracking.py to consume data from dictionaries instead of lists, as required by TensorFlow 2. This is a breaking change.

deepcell-tracking 0.2.7

0.2.7

Features

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

deepcell-tracking 0.2.6

deepcell-tracking 0.2.6

Bugfixes

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

deepcell-tracking 0.2.5

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%.

deepcell-tracking 0.2.4

This release addresses the ISBI text file related bugs and resolves the warnings generated by #16.

0.2.3 Improve compatibility with networkx>=2.4

Migrate ISBI utility functions from deepcell-tf to deepcell-tracking and update deprecated networkx functions to enable compatibility with networkx>=2.4.

0.2.2 Performance improvements with dynamic programming

This release improves the performance of track_cells by caching each cell's features for each frame. This reduces redundant calls to get_features and improves tracking performance by ~50%.

Various internal helper functions were added as well to improve readability and log timings of the major portions of tracking each frame.