Metadata-Version: 2.4
Name: FreeTrace
Version: 1.6.1.1
Summary: FreeTrace — single-molecule tracking with fBm inference
Author-email: Junwoo PARK <junwoo.park@sorbonne-universite.fr>
Maintainer-email: Junwoo PARK <junwoo.park@sorbonne-universite.fr>
License-Expression: GPL-3.0-or-later
Project-URL: Homepage, https://github.com/JunwooParkSaribu/FreeTrace
Project-URL: Repository, https://doi.org/10.5281/zenodo.13336251
Keywords: SPT,single-molecule,tracking
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: MacOS
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: numba
Requires-Dist: networkx
Requires-Dist: pandas
Requires-Dist: seaborn
Requires-Dist: tables
Requires-Dist: scikit-learn
Requires-Dist: scikit-image
Requires-Dist: scipy
Requires-Dist: opencv-python
Requires-Dist: matplotlib
Requires-Dist: imageio
Requires-Dist: tifffile
Requires-Dist: nd2
Requires-Dist: roifile
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Requires-Dist: tqdm
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Requires-Dist: tensorflow==2.14; python_version == "3.10" and sys_platform != "linux"
Requires-Dist: tensorflow[and-cuda]==2.14.1; python_version == "3.10" and sys_platform == "linux"
Requires-Dist: tensorflow==2.17; python_version == "3.11" and sys_platform != "linux"
Requires-Dist: tensorflow[and-cuda]==2.17; python_version == "3.11" and sys_platform == "linux"
Requires-Dist: tensorflow==2.18; python_version == "3.12" and sys_platform != "linux"
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Requires-Dist: cupy-cuda12x; extra == "gpu"
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Requires-Dist: tensorflow-metal; python_version < "3.13" and extra == "macos-gpu"
Provides-Extra: cli
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Dynamic: license-file


[![Static Badge](https://img.shields.io/badge/bioRxiv-FreeTrace-red)](https://doi.org/10.64898/2026.01.08.698486)
![Static Badge](https://img.shields.io/badge/%3E%3D3.10-1?style=flat&label=Python&color=blue)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13336251.svg)](https://doi.org/10.5281/zenodo.13336251)
![GitHub License](https://img.shields.io/github/license/JunwooParkSaribu/FreeTrace)

## FreeTrace

> [!IMPORTANT]  
> Requirements </br>
> - Windows(10/11) / GNU/Linux(Debian/Ubuntu) / MacOS(Sequoia/Tahoe)</br>
> - C compiler (clang)</br>
> - Python3.10 &#8593;</br>
> - GPU & Cuda12 on GNU/Linux with pre-trained [models](https://github.com/JunwooParkSaribu/FreeTrace/blob/main/FreeTrace/models/README.md) (recommended)</br>


> [!NOTE]  
> - PRE-REQUISITE: pre-installation and compilation, check [tutorial](https://github.com/JunwooParkSaribu/FreeTrace/blob/main/tutorial.ipynb). </br>
> - Check [compatibilities](https://github.com/JunwooParkSaribu/FreeTrace/blob/main/FreeTrace/models/README.md) of Python and Tensorflow to run FreeTrace with source code.</br>
> - Without GPU, FreeTrace is slow if it infers under fractional Brownian motion.</br>
> - Current version is stable with python 3.10 / 3.11 / 3.12</br>

<h2>Visualised FreeTrace results</h2>
<img width="825" src="https://github.com/JunwooParkSaribu/FreeTrace/blob/main/tmps/stars.gif">
<table border="0"> 
        <tr> 
            <td><img src="https://github.com/JunwooParkSaribu/FreeTrace/blob/main/tmps/trjs0.gif" width="230" height="230"></td> 
            <td><img src="https://github.com/JunwooParkSaribu/FreeTrace/blob/main/tmps/trjs1.gif" width="230" height="230"></td>
            <td><img src="https://github.com/JunwooParkSaribu/FreeTrace/blob/main/tmps/trjs2.gif" width="285" height="230"></td>
        </tr>  
</table>


&nbsp;&nbsp;<b>[FreeTrace](https://doi.org/10.64898/2026.01.08.698486)</b> infers individual trajectories from time-series images with reconnection of the detected particles under fBm.</br>

<h3> Contact person </h3>

<junwoo.park@sorbonne-universite.fr>

<h3> Contributors </h3>

> If you use this software, please cite it as below. </br>
```
@article {Park2026.01.08.698486,
	author = {Park, Junwoo and Sokolovska, Nataliya and Cabriel, Cl{\'e}ment and Kobayashi, Asaki and Corsin, Enora and Garcia Fernandez, Fabiola and Izeddin, Ignacio and Min{\'e}-Hattab, Judith},
	title = {Novel estimation of memory in molecular dynamics with extended and comprehensive single-molecule tracking software: FreeTrace},
	elocation-id = {2026.01.08.698486},
	year = {2026},
	doi = {10.64898/2026.01.08.698486},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2026/01/10/2026.01.08.698486},
	eprint = {https://www.biorxiv.org/content/early/2026/01/10/2026.01.08.698486.full.pdf},
	journal = {bioRxiv}
}
```
<br>
