{"id":19998758,"url":"https://github.com/quantixed/trackmater","last_synced_at":"2026-03-07T19:01:14.956Z","repository":{"id":47767837,"uuid":"453722113","full_name":"quantixed/TrackMateR","owner":"quantixed","description":"Analysis of TrackMate XML outputs in R","archived":false,"fork":false,"pushed_at":"2026-03-06T08:02:24.000Z","size":28339,"stargazers_count":17,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-03-06T11:55:17.601Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://quantixed.github.io/TrackMateR/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/quantixed.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-01-30T15:42:44.000Z","updated_at":"2026-03-06T07:51:03.000Z","dependencies_parsed_at":"2023-01-25T16:01:45.478Z","dependency_job_id":"3a373c04-8a64-4cc3-a36d-f12de0702c78","html_url":"https://github.com/quantixed/TrackMateR","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/quantixed/TrackMateR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FTrackMateR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FTrackMateR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FTrackMateR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FTrackMateR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quantixed","download_url":"https://codeload.github.com/quantixed/TrackMateR/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FTrackMateR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30226757,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-07T19:01:10.287Z","status":"ssl_error","status_checked_at":"2026-03-07T18:59:58.103Z","response_time":53,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2024-11-13T05:09:24.709Z","updated_at":"2026-03-07T19:01:14.939Z","avatar_url":"https://github.com/quantixed.png","language":"R","readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  message = FALSE\n)\n```\n\n# TrackMateR \u003ca href='https://quantixed.github.io/TrackMateR/'\u003e\u003cimg src='man/figures/logo.png' align=\"right\" height=\"131.5\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/quantixed/TrackMateR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/quantixed/TrackMateR/actions/workflows/R-CMD-check.yaml)\n[![DOI](https://zenodo.org/badge/453722113.svg)](https://zenodo.org/badge/latestdoi/453722113)\n\u003c!-- badges: end --\u003e\n\nAnalysis of TrackMate XML outputs in R.\n\n[TrackMate](https://imagej.net/plugins/trackmate/) is a single-particle tracking plugin for ImageJ/Fiji.\nThe standard output from a tracking session is in TrackMate XML format.\n\nThe goal of this R package is to import all of the data associated with the final filtered tracks in TrackMate for further analysis and visualization in R.\n\n## Installation\n\nOnce you have installed [R](https://cran.rstudio.com) and [RStudio Desktop](https://www.rstudio.com/products/rstudio/download/), you can install TrackMateR using devtools\n\n```{r gh-installation, eval = FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"quantixed/TrackMateR\")\n```\n\n## An Example\n\nA basic example is to load one TrackMate XML file, calibrate it (if needed) and analyse it.\n\n```{r example, fig.height = 8, fig.width = 8}\nlibrary(ggplot2)\nlibrary(TrackMateR)\n# an example file is provided, otherwise use file.choose()\nxmlPath \u003c- system.file(\"extdata\", \"ExampleTrackMateData.xml\", package=\"TrackMateR\")\n# read the TrackMate XML file into R using\ntmObj \u003c- readTrackMateXML(XMLpath = xmlPath)\n# Pixel size is actually 0.04 um and original data was 1 pixel, xyscalar = 0.04\ntmObj \u003c- correctTrackMateData(dataList = tmObj, xyscalar = 0.04, xyunit = \"um\")\n# generate a report\nreportDataset(tmObj)\n```\n\nTrackMateR can generate several different types of plot individually using commands or it can make them all automatically and create a report for you.\n\n- For details of how to make individual plots and/or tweak the default parameters, see `vignette(\"TrackMateR\")`\n- To see how to compare different datasets, see `vignette(\"comparison\")`\n- In order to rescale or recalibrate TrackMate data, see `vignette(\"recalibration\")`\n\n## Credits\n\n- TrackMateR builds on initial work by Julien Godet on [trackR](https://github.com/jgodet/trackR).\n- Méghane Sittewelle provided example TrackMate data and helped with testing TrackMateR.\n- The Fiji plug-in [TrackMate](https://github.com/trackmate-sc/TrackMate) is developed by Jean-Yves Tinevez.\n\n## Limitations, future development\n\n- TrackMateR is currently written for 2D data. 3D data is read but analysis is currently on the first two dimensions.\n- Addition of a dry run option to quickly report what data would be analysed by `compareDatasets()`.\n- Addition of number of tracks per frame and more advanced calculation of the density of tracks.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Ftrackmater","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantixed%2Ftrackmater","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Ftrackmater/lists"}