Package: laptrack
FeaturesProvides a robust particle tracking algorithm using the Linear Assignment Problem, with various cost functions for linking.See thepublicationandassociated repositoryfor the algorithm and parameter optimization byRay-Tune.RequirementsPython >= 3.8 is supported.
The software is tested against Python 3.8-3.12 in Ubuntu, and 3.12 in MacOS and Windows environments,
but the other combinations should also be fine. Pleasefile an issueif you encounter any problem.InstallationYou can installLapTrackviapipfromPyPI:$pipinstalllaptrackIn Google Colaboratory, try$pipinstall--upgradelaptrackspacyflaskmatplotlibto update the pre-installed packages.UsagePlease see theUsagefor details.
The example notebooks are provided indocs/examples.notebook nameshort descriptionGoogle Colaboratoryapi_example.ipynbIntroducing the package API by a simple example.bright_spots.ipynbApplication example: detecting bright spots by scikit-imageblob_logand tracking them.cell_segmentation.ipynbApplication example: tracking centroids of the segmented C2C12 cells undergoing divisions.napari_interactive_fix.ipynbIllustrates the usage of the ground-truth-preserved tracking withnapari.overlap_tracking.ipynbIllustrates the usage of the custom metric to use segmentation overlaps for tracking.TheAPI referencecovers the main classes and functions provided by LapTrack.ContributingContributions are very welcome.
To learn more, see theContributor Guide.LicenseDistributed under the terms of theThe 3-Clause BSD License,LapTrackis free and open source software.IssuesIf you encounter any problems,
pleasefile an issuealong with a detailed description.CreditsThis program implements a modified version of the algorithm in theK. Jaqaman et al. (2008).Inspired byTrackMatea lot. Seedocumentationfor its detailed algorithm, the2016 paper, and the2021 paper.The data indocs/examples/napari_interactive_fix_dataare generated by cropping images in10.5281/zenodo.6087728, which is distributed withCreative Commons Attribution 4.0 International.The data indocs/examples/cell_segmentation_dataare generated by cropping and resizing images inhttps://osf.io/ysaq2/, which is distributed withCreative Commons Attribution 4.0 International. See10.1038/sdata.2018.237for details.The data indocs/examples/overlap_tracking_datais generated by croppingsegmentation.npyinhttps://github.com/NoneqPhysLivingMatterLab/cell_interaction_gnn, which is distributed withApache License 2.0. See theoriginal paperfor details.The data indocs/examples/3D_tracking_datais generated by resizing iamges inhttps://bbbc.broadinstitute.org/BBBC050, which is distributed withCreative Commons Attribution 3.0 Unported License. See10.1038/s41540-020-00152-8for details.This project was generated from@cjolowicz’sHypermodern Python Cookiecuttertemplate.CitationIf you use this program for your research, please cite it and help us build more.@article{fukai_2022,title={{{LapTrack}}: Linear Assignment Particle Tracking with Tunable Metrics},shorttitle={{{LapTrack}}},author={Fukai, Yohsuke T and Kawaguchi, Kyogo},year={2022},month=dec,journal={Bioinformatics},pages={btac799},issn={1367-4803},doi={10.1093/bioinformatics/btac799},}@misc{laptrack,author={Yohsuke T. Fukai},title={laptrack},year={2021},url={https://doi.org/10.5281/zenodo.5519537},}