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**.

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# 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**.

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## 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**.

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## 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.

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## 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**.

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## 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.

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## 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.

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# 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

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# 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

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# Citation

Please cite the associated publication when using these datasets.