Metadata-Version: 2.4
Name: TrackRefiner
Version: 1.2.7
Summary: A precision tracking tool for bacillus cell tracking
Home-page: https://github.com/ingallslab/Trackrefiner
Author: Atiyeh Ahmadi
Author-email: Atiyeh Ahmadi <a94ahmad@uwaterloo.ca>
License: BSD 3-Clause
Project-URL: homepage, https://github.com/ingallslab/Trackrefiner
Project-URL: tutorial, https://github.com/ingallslab/Trackrefiner/wiki
Project-URL: documentation, https://github.com/ingallslab/Trackrefiner/tree/main/docs/html
Project-URL: faq, https://github.com/ingallslab/Trackrefiner/issues
Project-URL: issues, https://github.com/ingallslab/Trackrefiner/issues
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Environment :: Console
Classifier: Environment :: X11 Applications :: Qt
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
Requires-Dist: numpy==1.26.4
Requires-Dist: scipy
Requires-Dist: pandas>=2.2.2
Requires-Dist: scikit-learn
Requires-Dist: matplotlib
Requires-Dist: opencv-python
Requires-Dist: scikit-image
Requires-Dist: psutil
Requires-Dist: seaborn
Requires-Dist: PyQt5
Dynamic: author
Dynamic: home-page
Dynamic: requires-python

# 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) |


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

<div align="justify"> 
  
**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)

The following sections provide more details on:
1.	<a href='https://github.com/Ati-74/Trackrefiner/wiki/Installation-Guide'>Installation Guide</a>
2.	<a href='https://github.com/Ati-74/Trackrefiner/wiki/How-to-Run-TrackRefiner'>How to Run TrackRefiner</a>
3.	<a href='https://github.com/Ati-74/Trackrefiner/wiki/Tutorial'>Tutorial</a>
4.	<a href='https://github.com/Ati-74/Trackrefiner/wiki/Reported-Feature-Explanations'>Reported Feature Explanations</a>
5.	<a href='https://github.com/Ati-74/Trackrefiner/wiki/TrackRefiner-Outputs'>TrackRefiner Outputs</a>
6.	<a href='https://github.com/Ati-74/Trackrefiner/wiki/Visualizing-and-Editing-Bacterial-Tracking'>Visualizing and Editing Bacterial Tracking</a>
7.	<a href='https://github.com/Ati-74/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>

</div>
