TrackRefiner 1.3
A precision tracking tool for bacillus cell tracking
License: BSD 3-Clause
Requires Python: <3.13,>=3.9

# Trackrefiner: A precision tracking tool for bacillus cell tracking

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| Package | [![PyPI Latest Release](https://img.shields.io/pypi/v/trackrefiner)](https://pypi.org/project/TrackRefiner/) [![Conda Latest Release](https://img.shields.io/conda/v/ingalls-lab/trackrefiner)](https://anaconda.org/ingalls-lab/trackrefiner) |
| Meta | [![DOI](https://img.shields.io/badge/DOI-10.1101/2025.02.13.637647-blue.svg)](https://www.biorxiv.org/content/10.1101/2025.02.13.637647v1) [![License - BSD 3-Clause](https://img.shields.io/github/license/ati-74/trackrefiner)](https://github.com/Ati-74/Trackrefiner/blob/main/LICENSE.md) |


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  <img src="https://github.com/user-attachments/assets/4d8233d0-e699-4c7b-9fc3-6a25920e515f" alt="image" width="30%"/>
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**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:

![image](https://github.com/user-attachments/assets/27ab0b8c-5437-4376-80a9-13c5163ec20e)

## 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:**  
    ```bash
    trackrefiner-cli
    ```
  - **Graphical User Interface:**  
    ```bash
    trackrefiner-gui
    ```

- **Manual editing of tracking results:**
```
trackrefiner-track-editor
```

## How to Use TrackRefiner

The following sections provide more details on:
1.	<a href='https://github.com/ingallslab/Trackrefiner/wiki/Installation-Guide'>Installation Guide</a>
2.	<a href='https://github.com/ingallslab/Trackrefiner/wiki/How-to-Run-TrackRefiner'>How to Run TrackRefiner</a>
3.	<a href='https://github.com/ingallslab/Trackrefiner/wiki/Tutorial'>Tutorial</a>
4.	<a href='https://github.com/ingallslab/Trackrefiner/wiki/Reported-Feature-Explanations'>Reported Feature Explanations</a>
5.	<a href='https://github.com/ingallslab/Trackrefiner/wiki/TrackRefiner-Outputs'>TrackRefiner Outputs</a>
6.	<a href='https://github.com/ingallslab/Trackrefiner/wiki/Visualizing-and-Editing-Bacterial-Tracking'>Visualizing and Editing Bacterial Tracking</a>
7.	<a href='https://github.com/ingallslab/Trackrefiner/wiki/Developers'>Developers</a>

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

<a href='https://www.biorxiv.org/content/10.1101/2025.02.13.637647v1'>TrackRefiner: A tool for refinement of bacillus cell tracking data</a>

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