{"id":13716931,"url":"https://github.com/trackmate-sc/TrackMate","last_synced_at":"2025-05-07T06:31:48.090Z","repository":{"id":12649832,"uuid":"15321451","full_name":"trackmate-sc/TrackMate","owner":"trackmate-sc","description":"TrackMate is your buddy for your everyday tracking.","archived":false,"fork":false,"pushed_at":"2025-04-29T06:55:03.000Z","size":12991,"stargazers_count":189,"open_issues_count":26,"forks_count":79,"subscribers_count":20,"default_branch":"master","last_synced_at":"2025-04-29T07:44:56.512Z","etag":null,"topics":["fiji-plugin","image-analysis","single-particle-tracking"],"latest_commit_sha":null,"homepage":"https://imagej.net/plugins/trackmate","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/trackmate-sc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2013-12-19T20:01:53.000Z","updated_at":"2025-04-23T14:08:51.000Z","dependencies_parsed_at":"2023-02-10T16:00:29.778Z","dependency_job_id":"f71e69f8-110c-46a1-9acc-a9f59540d9c3","html_url":"https://github.com/trackmate-sc/TrackMate","commit_stats":null,"previous_names":["fiji/trackmate"],"tags_count":94,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trackmate-sc%2FTrackMate","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trackmate-sc%2FTrackMate/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trackmate-sc%2FTrackMate/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trackmate-sc%2FTrackMate/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/trackmate-sc","download_url":"https://codeload.github.com/trackmate-sc/TrackMate/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252826881,"owners_count":21810197,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["fiji-plugin","image-analysis","single-particle-tracking"],"created_at":"2024-08-03T00:01:15.758Z","updated_at":"2025-05-07T06:31:46.362Z","avatar_url":"https://github.com/trackmate-sc.png","language":"Java","funding_links":[],"categories":["Cell migration and particle tracking"],"sub_categories":[],"readme":"[![Build Status](https://github.com/trackmate-sc/TrackMate/actions/workflows/build.yml/badge.svg)](https://github.com/trackmate-sc/TrackMate/actions/workflows/build.yml)\n[![Image.sc Forum](https://img.shields.io/badge/dynamic/json.svg?label=forum\u0026amp;url=https%3A%2F%2Fforum.image.sc%2Ftags%2Ftrackmate.json\u0026amp;query=%24.topic_list.tags.0.topic_count\u0026amp;colorB=green\u0026amp;\u0026amp;suffix=%20topics\u0026amp;logo=data:image/png;base64,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)](https://forum.image.sc/tag/trackmate)\n\n![TrackMate logo](https://imagej.net/media/logos/trackmate-300p.png)\n\n\nTrackMate\n=========\n\nTrackMate is your buddy for your everyday tracking.\n\n\nCitation\n--------\n\nPlease note that TrackMate is available through Fiji, and is based on a publication. If you use it successfully for your research please be so kind to cite our work:\n\nJean-Yves Tinevez, Nick Perry, Johannes Schindelin, Genevieve M. Hoopes, Gregory D. Reynolds, Emmanuel Laplantine, Sebastian Y. Bednarek, Spencer L. Shorte, Kevin W. Eliceiri, __TrackMate: An open and extensible platform for single-particle tracking__, Methods, Available online 3 October 2016, ISSN 1046-2023, http://dx.doi.org/10.1016/j.ymeth.2016.09.016. (http://www.sciencedirect.com/science/article/pii/S1046202316303346)\n\n\nSingle Particle Tracking\n------------------------\n\nTrackMate provides the tools to perform single particle tracking (SPT). SPT is\nan image analysis challenge where the goal is to segment and follow over time\nsome labelled, spot-like structures. Each spot is segmented in multiple frames\nand its trajectory is reconstructed by assigning it an identity over these\nframes, in the shape of a track. These tracks can then be either visualized or\nyield further analysis results such as velocity, total displacement, diffusion\ncharacteristics, division events, etc...\n\nTrackMate can deal with single particles, or spot-like objects. They are bright\nobjects over a dark background for which the object contour shape is not\nimportant, but for which the main information can be extracted from the X,Y,Z\ncoordinates over time. Examples include sub-resolution fluorescent spots,\nlabelled traffic vesicles, nuclei or cells imaged at low resolution.\n\nThough these objects are solely represented by a X,Y,Z,T coordinates array,\nTrackMate can compute numerical features for each spot, given its coordinates\nand a radius. For instance, the mean, max, min and median intensity will be\ncomputed, as well as the estimated radius and orientation for each spot,\nallowing to follow how these feature evolves over time for one object.\n\n\nTrackMate goals\n---------------\n\nIts development focuses on achieving two concomitant goals:\n\n### For users ###\n\nTrackMate aims at offering a generic solution that works out of the box,\nthrough a simple and sensible user interface.\n\nThe tracking process is divided in a series of steps, through which you will be\nguided thanks to a wizard-like GUI. It privileges tracking schemes where the\nsegmentation step is decoupled from the particle-linking step.\n\nThe segmentation / filtering / particle-linking processes and results are\nvisualized immediately in 2D or 3D, allowing to judge their efficiency and\nadjust their control parameters. The visualization tools are the one shipped\nwith Fiji and interact nicely with others plugin.\n\nSeveral automated segmentation and linking algorithms are provided. But you are\nalso offered to edit the results manually, or even to completely skip the\nautomatic steps, and perform fully manual segmentation and/or linking.\n\nSome tools for track and spot analysis are included. Various plots can be made\ndirectly from the plugin and for instance used to derive numerical results from\nthe tracks. If they are not enough, functions are provided to export the whole\nresults to other analysis software such as MATLAB.\n\nTrackMate relies on several different libraries and plugins for data\nmanipulation, analysis and visualization. This can be a pitfall when\ndistributing a complex plugin, but this is where the Fiji magic comes into\nplay. All dependencies are dealt with by through the Fiji updater. Installing\nTrackMate is easy as calling the Fiji Updater, and the plugin must work out of\nthe box. If this does not work for you, then it is a bug and we commit to fix\nit.\n\nA strong emphasis is made on performance, and TrackMate will take advantage of\nmulti-cores hardware.\n\n### For developers ###\n\nHave you ever wanted to develop your own segmentation and/or particle-linking\nalgorithm, but wanted to avoid the painful burden to also write a GUI, several\nvisualization tools, analysis tools and exporting facilities? Then TrackMate is\nfor you.\n\nWe spent a considerable amount of time making TrackMate extensible in every\naspect. It has a very modular design, that makes it easy to extend. You can for\ninstance develop your own segmentation algorithm, extend TrackMate to include\nit, and benefit from the visualization tools and the GUI already there. Here is\na list of the components you can extend and customize:\n\n* detection algorithms\n* particle-linking algorithms\n* numerical features for spots (such as mean intensity, etc..)\n* numerical features for links (such as velocity, orientation, etc..)\n* numerical features for tracks (total displacement, length, etc...)\n* visualization tools\n* post-processing actions (exporting, data massaging, etc...)\n\nYou can even modify the GUI, and remove, edit or insert new steps in the\nwizard. This can be useful for instance if you want to implement a tracking\nscheme that solves simultaneously the segmentation part and the particle\nlinking part, but still want to take advantage of TrackMate components.\n\nDo you want to make your new algorithms usable by the reviewers of your\nsubmitted paper? Upload your extended version of TrackMate to a private update\nsite, as explained here, then send the link to the reviewers. Now that the\npaper has been accepted (congratulations), you want to make it accessible to\nanyone? Just put the link to the update site in the article. All of this can\nhappen without us even noticing.\n\nTrackMate was developed to serve as a tool for Life-Science image analysis\ncommunity, so that new tracking tools can be developed more easily and quickly,\nand so that end-users can use them to perform their own research. We will\nsupport you if need help to reuse it.\n\nFor details, please see http://fiji.sc/TrackMate\n\n\n## Star History\n\n[![Star History Chart](https://api.star-history.com/svg?repos=trackmate-sc/TrackMate\u0026type=Date)](https://star-history.com/#trackmate-sc/TrackMate\u0026Date)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrackmate-sc%2FTrackMate","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftrackmate-sc%2FTrackMate","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrackmate-sc%2FTrackMate/lists"}