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Tracking"],"sub_categories":["Software tools"],"readme":"LapTrack\n========\n\n|PyPI| |Status| |Python Version| |License| |Download|\n\n|Read the Docs| |Tests| |Codecov| |pre-commit| |Ruff|\n\n|Publication| |Preprint| |Zenodo|\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/laptrack.svg\n   :target: https://pypi.org/project/laptrack/\n   :alt: PyPI\n.. |Status| image:: https://img.shields.io/pypi/status/laptrack.svg\n   :target: https://pypi.org/project/laptrack/\n   :alt: Status\n.. |Python Version| image:: https://img.shields.io/pypi/pyversions/laptrack\n   :target: https://pypi.org/project/laptrack\n   :alt: Python Version\n.. |License| image:: https://img.shields.io/pypi/l/laptrack\n   :target: https://opensource.org/licenses/BSD-3-Clause\n   :alt: License\n.. |Download| image:: https://img.shields.io/pepy/dt/laptrack\n   :target: https://pypi.org/project/laptrack\n   :alt: Total Download\n.. |Read the Docs| image:: https://img.shields.io/readthedocs/laptrack/latest.svg?label=Read%20the%20Docs\n   :target: https://laptrack.readthedocs.io/\n   :alt: Read the documentation at https://laptrack.readthedocs.io/\n.. |Tests| image:: https://github.com/yfukai/laptrack/workflows/Tests/badge.svg\n   :target: https://github.com/yfukai/laptrack/actions?workflow=Tests\n   :alt: Tests\n.. |Codecov| image:: https://codecov.io/gh/yfukai/laptrack/branch/main/graph/badge.svg\n   :target: https://codecov.io/gh/yfukai/laptrack\n   :alt: Codecov\n.. |pre-commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit\u0026logoColor=white\n   :target: https://github.com/pre-commit/pre-commit\n   :alt: pre-commit\n.. |Ruff| image:: https://img.shields.io/badge/linting-ruff-red?logo=ruff\n   :target: https://github.com/astral-sh/ruff\n   :alt: Ruff\n.. |Zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5519537.svg\n   :target: https://doi.org/10.5281/zenodo.5519537\n   :alt: Zenodo\n.. |Publication| image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtac799-167DA4\n   :target: https://doi.org/10.1093/bioinformatics/btac799\n   :alt: Bioinformatics\n.. |Preprint| image:: https://img.shields.io/badge/bioRxiv-10.1101%2F2022.10.05.511038-bd2736\n   :target: https://doi.org/10.1101/2022.10.05.511038\n   :alt: bioRxiv\n\nFeatures\n--------\n\nProvides a robust particle tracking algorithm using the Linear Assignment Problem, with various cost functions for linking.\n\nSee the `publication`_ and `associated repository`_ for the algorithm and parameter optimization by `Ray-Tune`_.\n\nRequirements\n------------\n\nPython \u003e= 3.10 is supported.\nThe software is tested against Python 3.10-3.14 in Ubuntu, and 3.14 in MacOS and Windows environments,\nbut the other combinations should also be fine. Please `file an issue`_ if you encounter any problem.\n\nInstallation\n------------\n\nYou can install *LapTrack* via pip_ from PyPI_:\n\n.. code:: console\n\n   $ pip install laptrack\n\nIn Google Colaboratory, try\n\n.. code:: console\n\n   $ pip install --upgrade laptrack spacy flask matplotlib\n\nto update the pre-installed packages.\n\n\nUsage\n-----\n\nPlease see the Usage_ for details.\nThe example notebooks are provided in `docs/examples \u003chttps://github.com/yfukai/laptrack/tree/main/docs/examples\u003e`_.\n\n\n+--------------------------------+--------------------------------------------------------------------------------------------+----------------------+\n| notebook name                  | short description                                                                          | Google Colaboratory  |\n+================================+============================================================================================+======================+\n| `api_example.ipynb`_           | Introducing the package API by a simple example.                                           ||colab|               |\n+--------------------------------+--------------------------------------------------------------------------------------------+----------------------+\n| `bright_spots.ipynb`_          | Application example: detecting bright spots by scikit-image `blob_log` and tracking them.  |                      |\n+--------------------------------+--------------------------------------------------------------------------------------------+----------------------+\n| `cell_segmentation.ipynb`_     | Application example: tracking centroids of the segmented C2C12 cells undergoing divisions. |                      |\n+--------------------------------+--------------------------------------------------------------------------------------------+----------------------+\n| `napari_interactive_fix.ipynb`_| Illustrates the usage of the ground-truth-preserved tracking with `napari`.                |                      |\n+--------------------------------+--------------------------------------------------------------------------------------------+----------------------+\n| `overlap_tracking.ipynb`_      | Illustrates the usage of the custom metric to use segmentation overlaps for tracking.      |                      |\n+--------------------------------+--------------------------------------------------------------------------------------------+----------------------+\n\n.. _api_example.ipynb:            https://github.com/yfukai/laptrack/tree/main/docs/examples/api_example.ipynb\n.. _bright_spots.ipynb:           https://github.com/yfukai/laptrack/tree/main/docs/examples/bright_spots.ipynb\n.. _cell_segmentation.ipynb:      https://github.com/yfukai/laptrack/tree/main/docs/examples/cell_segmentation.ipynb\n.. _napari_interactive_fix.ipynb: https://github.com/yfukai/laptrack/tree/main/docs/examples/napari_interactive_fix.ipynb\n.. _overlap_tracking.ipynb:       https://github.com/yfukai/laptrack/tree/main/docs/examples/overlap_tracking.ipynb\n\n.. |colab| image:: https://colab.research.google.com/assets/colab-badge.svg\n           :target: https://colab.research.google.com/github/yfukai/laptrack/blob/main/docs/examples/api_example.ipynb\n\nThe `API reference \u003chttps://laptrack.readthedocs.io/en/latest/reference.html\u003e`_ covers the main classes and functions provided by LapTrack.\n\nContributing\n------------\n\nContributions are very welcome.\nTo learn more, see the `Contributor Guide`_.\n\n\nLicense\n-------\n\nDistributed under the terms of the `The 3-Clause BSD License`_,\n*LapTrack* is free and open source software.\n\n\nIssues\n------\n\nIf you encounter any problems,\nplease `file an issue \u003chttps://github.com/yfukai/laptrack/issues\u003e`_ along with a detailed description.\n\n\nCredits\n-------\n\n- This program implements a modified version of the algorithm in the `K. Jaqaman et al. (2008)`_.\n\n- Inspired by TrackMate_ a lot. See documentation_ for its detailed algorithm, the `2016 paper`_, and the `2021 paper`_.\n\n- The data in `docs/examples/napari_interactive_fix_data` are generated by cropping images in `10.5281/zenodo.6087728 \u003chttps://doi.org/10.5281/zenodo.6087728\u003e`_, which is distributed with `Creative Commons Attribution 4.0 International`_.\n\n- The data in `docs/examples/cell_segmentation_data` are generated by cropping and resizing images in https://osf.io/ysaq2/, which is distributed with `Creative Commons Attribution 4.0 International`_. See `10.1038/sdata.2018.237 \u003chttps://doi.org/10.1038/sdata.2018.237\u003e`_ for details.\n\n- The data in `docs/examples/overlap_tracking_data` is generated by cropping `segmentation.npy` in https://github.com/NoneqPhysLivingMatterLab/cell_interaction_gnn, which is distributed with `Apache License 2.0`_. See the `original paper \u003chttps://doi.org/10.1371/journal.pcbi.1010477\u003e`_ for details.\n\n- The data in `docs/examples/3D_tracking_data` is generated by resizing iamges in https://bbbc.broadinstitute.org/BBBC050 , which is distributed with `Creative Commons Attribution 3.0 Unported License`_. See `10.1038/s41540-020-00152-8 \u003chttps://doi.org/10.1038/s41540-020-00152-8\u003e`_ for details.\n\n- This project was generated from `@cjolowicz`_'s `Hypermodern Python Cookiecutter`_ template.\n\n\nCitation\n--------\n\nIf you use this program for your research, please cite it and help us build more.\n\n.. code-block::\n\n   @article{fukai_2022,\n     title = {{{LapTrack}}: Linear Assignment Particle Tracking with Tunable Metrics},\n     shorttitle = {{{LapTrack}}},\n     author = {Fukai, Yohsuke T and Kawaguchi, Kyogo},\n     year = {2022},\n     month = dec,\n     journal = {Bioinformatics},\n     pages = {btac799},\n     issn = {1367-4803},\n     doi = {10.1093/bioinformatics/btac799},\n   }\n\n   @misc{laptrack,\n      author = {Yohsuke T. Fukai},\n      title = {laptrack},\n      year  = {2021},\n      url   = {https://doi.org/10.5281/zenodo.5519537},\n   }\n\n.. _publication: https://doi.org/10.1093/bioinformatics/btac799\n.. _associated repository: https://github.com/NoneqPhysLivingMatterLab/laptrack-optimisation\n.. _Ray-Tune: https://www.ray.io/ray-tune\n\n.. _K. Jaqaman et al. (2008): https://www.nature.com/articles/nmeth.1237\n.. _TrackMate: https://imagej.net/plugins/trackmate/\n.. _documentation: https://imagej.net/plugins/trackmate/algorithms\n.. _2016 paper: https://doi.org/10.1016/j.ymeth.2016.09.016\n.. _2021 paper: https://doi.org/10.1101/2021.09.03.458852\n.. _Creative Commons Attribution 4.0 International: https://creativecommons.org/licenses/by/4.0/legalcode\n.. _Creative Commons Attribution 3.0 Unported License: https://creativecommons.org/licenses/by/3.0/legalcode\n.. _The 3-Clause BSD License: https://opensource.org/licenses/BSD-3-Clause\n.. _Apache License 2.0: https://opensource.org/licenses/Apache-2.0\n\n.. _@cjolowicz: https://github.com/cjolowicz\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _PyPI: https://pypi.org/\n.. _Hypermodern Python Cookiecutter: https://github.com/cjolowicz/cookiecutter-hypermodern-python\n.. _pip: https://pip.pypa.io/\n.. github-only\n.. _Contributor Guide: CONTRIBUTING.rst\n.. _Usage: https://laptrack.readthedocs.io/en/latest/usage.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fyfukai%2Flaptrack","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fyfukai%2Flaptrack","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fyfukai%2Flaptrack/lists"}