TrackRefiner 1.3

A precision tracking tool for bacillus cell tracking

Trackrefiner: A precision tracking tool for bacillus cell tracking

Package
Meta

TrackRefiner is a post-processing tool specifically designed to refine the tracking outputs of CellProfiler, a widely used image processing tool. It improves tracking accuracy by refining segmentation and tracking outputs, pruning incorrect links, and adding missing ones. TrackRefiner combines traditional tracking methods with machine learning classifiers, requiring minimal user input while leveraging a data-driven approach to optimize results.

The general pipeline of TrackRefiner is illustrated in the following figure:

Key Commands

TrackRefiner provides both command-line tools and graphical interfaces for tracking refinement and manual editing of tracking results.
Use -h with commands to view available options.

• Remove jitter from dataset images:

  trackrefiner-jitter-remover
  

• Run tracking refinement:

  • Command-Line Interface:

    trackrefiner-cli
    

  • Graphical User Interface:

    trackrefiner-gui
    

• Manual editing of tracking results:

trackrefiner-track-editor

How to Use TrackRefiner

The following sections provide more details on:

1. Installation Guide
2. How to Run TrackRefiner
3. Tutorial
4. Reported Feature Explanations
5. TrackRefiner Outputs
6. Visualizing and Editing Bacterial Tracking
7. Developers

Citation

If you use TrackRefiner in your research, please cite it using the following reference:

TrackRefiner: A tool for refinement of bacillus cell tracking data