Scripts for "LapTrack: Linear assignment particle tracking with tunable metrics"

Parameter optimization for LapTrack with Ray-Tune.

Executing the analysis

conda env create -f conda_env_minimum.yaml
conda activate optlaptrack

python execute.py --n-jobs=1 conditions_drift.yaml # for the cell migration dataset
python execute.py --n-jobs=1 conditions_synthetic.yaml # for the coloured particles dataset
python execute.py --n-jobs=1 conditions_homeostasis.yaml # for the mouse epidermis dataset

cd tracking_scripts
python a1_homeostasis_simple_LAP_baseline_grid.py # to perform grid search for the mouse epidermis dataset
python a2-1_yeast_toolkit_benchmark.py # to perform grid search for the Yeast Image Toolkit dataset
# execute a2-2_yeast_toolkit_benchmark_evaluation_platform.py 
# with following the instruction at the file top
# to evaluate the scores for the Yeast Image Toolkit dataset results
python a3_C2C12_simple_LAP_baseline_grid.py # to perform grid search for the C2C12 dataset

Directories

• data the organized datasets
• tracking_scripts the tracking and plotting scripts
• setting_yaml YAML setting files for tracking scripts
• results the tracking results
• plots the result plots

Tracking scripts

Located in tracking_scripts, executed via execute.py.

• 01_simple_LAP.py LAP with Euclidean distance only
• 02_simple_LAP_with_drift.py LAP with Euclidean distance and the drift term
• 03_simple_LAP_with_similarity-simple.py LAP with the feature Euclidean distance term
• 04_simple_LAP_with_overlap_dist_sum.py LAP with overlap cost function

Plotting scripts

Located in tracking_scripts, executed as Jupyter notebooks in, e.g., Visual Studio Code.

• z1-1_make_grid_search_plots.py Generate Fig. 2(b), S1, and S3.
• z1-2_make_yeast_grid_search_plots.py Generate Fig. S2.
• z2_CellMigration_summarize_results.py Generate Fig. 2(d) and S2.
• z3_synthetic_summarize_results.py Generate Fig. 2(f) and S3.
• z4_homeostasis_summarize_results.py Generate Fig. 2(g).
• z5_summarize_properties.py Summarize particle counts.

Other scripts

Located in tracking_scripts.

• a1_homeostasis_simple_LAP_baseline_grid.py Performs grid search for the mouse epidermis dataset.
• a2-1_yeast_toolkit_benchmark.py Performs grid search for the Yeast Image Toolkit dataset.
• a2-2_yeast_toolkit_benchmark_evaluation_platform.py Evaluate tracking scores for the Yeast Image Toolkit dataset results (generated by a2-1_yeast_toolkit_benchmark.py).
• a3_C2C12_simple_LAP_baseline_grid.py Performs grid search for the C2C12 dataset.

Datasets

Located in data.

• CellMigration Data for the cell migration dataset.
• homeostasis Data for the mouse epidermis dataset.
• synthetic Data for the coloured particles dataset.
• yeast_image_toolkit_benchmark Data for the Yeast Image Toolkit dataset.
• C2C12 Data for the C2C12 dataset.

Results

Located in results.

• CellMigration_use_0.05 Results for the cell migration dataset.
• homeostasis Results for the mouse epidermis dataset.
• homeostasis_grid_search Results for parameter grid search with the mouse epidermis dataset.
• synthetic Reksults for the coloured particles dataset.
• yeast_image_toolkit_benchmark Results for parameter grid search with the Yeast Image Toolkit dataset.
• C2C12_grid_search Results for parameter grid search with the C2C12 dataset.

Interactive annotation example

• The example for interactive annotation with napari is located in The LapTrack repository.

Credits

• The data in data/CellMigration are generated from data in 10.5281/zenodo.6087728, which are distributed with Creative Commons Attribution 4.0 International.
• The data in data/homeostasis are generated from data in the Cell interaction paper repository.
• The data in data/C2C12 are generated from data in https://osf.io/ysaq2/, which is distributed with Creative Commons Attribution 4.0 International. See 10.1038/sdata.2018.237 for details.
• The data in data/yeast_image_toolkit_benchmark is generated from data in Yeast Image Toolkit website with the author consent.

Note

To reproduce the publication result in the precisely same environment, the following command should be executed at the commit 160a34f20f3e6a6ac4f894eb9fe4f6092a747843.

python execute.py --n-jobs=1 conditions_drift.yaml # for the cell migration dataset
python execute.py --n-jobs=1 conditions_synthetic.yaml # for the coloured particles dataset
python execute.py --n-jobs=1 conditions_homeostasis.yaml # for the mouse epidermis dataset

cd tracking_scripts
python a1_homeostasis_simple_LAP_baseline_grid.py # to perform grid search for the mouse epidermis dataset