Awesome Tracking Tools

Contributing

To contribute to our awesome list, please open an issue or PR on our website repo.

A curated list of open‑source software, libraries, datasets, and resources for live‑cell tracking, lineaging, and trajectory analysis in bioimage data.

Software

Legend

• Interface: API , GUI
• Task: Detect , Track , Edit , Visualize

Name	Description	Language	Interface	Task
btrack	Bayesian multi-object tracker for crowded scenes	Python
Motile	Integer-linear-programming library for globally optimised tracking	Python
Motile Tracker	An application for interactive for tracking with motile	Python
LapTrack	Linear-assignment-problem tracker with tunable costs	Python
TrackAstra	Transformer-based cell tracker for segmented masks	Python
Caliban	Deep-learning based nuclear segmentation and tracking	Python
Ultrack	Scalable 2D/3D tracking under segmentation uncertainty	Python
TrackMate	Everyday object-tracking plugin for Fiji	Java
Mastadon	Next-generation interactive tracking for large datasets	Java
ELEPHANT	Incremental deep-learning 3D tracking on Mastodon	Python / Fiji
inTRACKtive	Interactive web lineage-tree visualiser.	Python
track_gardener	Napari plugin with tools for manual correction of tracking data.	Python
divisualization	Visualize cell tracking edge errors computed via traccuracy in napari.	Python

Benchmarks & Metrics

• Cell Tracking Challenge — Gold‑standard benchmark datasets & metrics.
• traccuracy — Python library for evaluating cell tracking solutions.

Datasets

• Cell Tracking Challenge datasets — 2D/3D annotated sequences for benchmarking.
• DeepSea dataset — 47 time‑lapse sequences across three cell types.
• Phase‑Contrast Myoblast Lineage dataset — 48 long‑term phase‑contrast movies with ground truth.

File Formats

• GEFF — Standardized graph exchange format for tracking data.