Example dataset and results for Tui, a multi-generational and expert-correctable tracker for cellular dynamics

# Tui Example Datasets and Tracking Results This repository provides example datasets and tracking results used to demonstrate the functionality of **Tui**, a multigenerational and expert-correctable cell tracking framework designed to reconstruct complex lineage dynamics including mitosis and fusion events. The repository contains both **synthetic benchmark datasets** and **experimental live-cell imaging datasets**, along with segmentation masks and example tracking outputs generated by the Tui framework. These resources are intended to facilitate **method reproducibility, benchmarking, and demonstration of the Tui tracking workflow**. --- # Repository Contents ## 1. Synthetic_200frames_41mitosis_1fusion.zip Synthetic benchmark dataset containing simulated cell trajectories with controlled lineage events. Dataset characteristics: - 200 time-lapse frames- 41 mitosis events- 1 programmed fusion event- full ground-truth lineage annotation in CTC format This dataset simulates realistic cell behaviors including: - migration- mitosis (1→2 events)- fusion (2→1 events)- appearance and disappearance The dataset allows validation of tracking algorithms under **known ground-truth lineage structures**. --- ## 2. synthetic_cell_6fusions.zip Synthetic dataset specifically designed to test **fusion tracking capability**. Dataset characteristics: - multiple controlled lineage topologies- 6 programmed fusion events- 34 mitosis events- 200 frames This dataset demonstrates the ability of the Tui ILP-based tracker to correctly resolve **M→1 fusion events and 1→2 mitosis events simultaneously**. --- ## 3. DIC-C2DH_HeLa_dataset.zip Experimental dataset from the **Cell Tracking Challenge (CTC)**: Dataset characteristics: - Differential interference contrast microscopy (DIC)- 83 frames per sequence- cell population growing from ~12 to ~21 cells per field of view- 9 mitosis events- lineage depth up to 2 generations- confluency increasing from ~39.6% to ~62.2% The dataset includes: - microscopy images- Detectron2-generated segmentation masks- CTC ground-truth lineage annotations This dataset represents **moderately dense proliferating cell populations** used to evaluate lineage reconstruction under realistic microscopy conditions. --- ## 4. T98G_electrotaxis.zip Experimental dataset of **T98G glioblastoma cells undergoing electrotaxis** under a direct current electric field. Dataset characteristics: - 37 frames (~6 hours)- ~70–72 cells per field of view- 8 mitosis events- lineage depth up to 2 generations- confluency ~18–25% The dataset includes: - time-lapse microscopy images- human-curated segmentation masks- manually curated lineage annotations These annotations provide **expert-validated ground truth** for evaluating tracking performance in directional cell migration experiments. Two segmentation variants are provided: - human-curated segmentation masks- Detectron2-generated masks This allows comparison between **expert segmentation and automated pipelines**. --- ## 5. Fluo-N2DH-SIM+.zip Fluorescence microscopy dataset from the **Cell Tracking Challenge**. Dataset characteristics: - 65 frames- 30–41 cells per field of view- 29 mitosis events- lineage depth up to 3 generations This dataset provides a **dense proliferation scenario with frequent mitotic events**, making it useful for benchmarking lineage reconstruction performance. --- ## 6. Example_results.zip Example tracking outputs generated using the **Tui ILP-based tracking framework**. Included results: - reconstructed cell trajectories- lineage relationships- tracking graphs- example outputs for both synthetic and experimental datasets These files demonstrate how Tui reconstructs **multi-generational lineage structures**, including complex events such as mitosis and fusion. --- # Intended Use These datasets are provided to help users: - reproduce example tracking workflows- benchmark alternative tracking algorithms- evaluate tracking robustness under synthetic and experimental conditions- explore multigenerational lineage reconstruction including mitosis and fusion events --- # Related Software **Tui — A Multigenerational and Expert-Correctable Tracker for Cellular Dynamics** The Tui framework reconstructs lineage graphs using an **integer linear programming (ILP)** formulation capable of modeling: - cell transitions- mitosis- fusion- appearance- disappearance --- # Citation Please cite the associated publication when using these datasets.