Tracking Challenge Utils

Utilities for the whole embryo tracking challenge, providing tools for visualizing and evaluating cell tracking datasets.

Requirements

• Python >=3.11
• uv for dependency management

Installation

Clone the repository and install dependencies:

git clone git@github.com:royerlab/tracking-challenge-utils.git
cd tracking-challenge-utils
uv sync

Examples

IMPORTANT: The example requires you to manually change the DATA_DIR variable to the path of the dataset you want to use.

Basic Dataset Visualization

View embryo images and ground truth tracks:

uv run examples/basic.py

This example:

• Loads a tracking dataset
• Displays the image data in napari
• Shows ground truth tracks as both connected tracks and individual points

Naive Tracking Pipeline

IMPORTANT: This is a proof of concept but not a competitive baseline for the challenge.

Run a complete cell detection and tracking pipeline:

uv run examples/naive_tracking.py

This example demonstrates:

• Naive cell detection using Gaussian filtering and peak detection
• Distance-based cell linking between frames
• Track evaluation against ground truth
• Visualization of detected cells, solution tracks, and ground truth