https://github.com/quantixed/TrackMateR

Analysis of TrackMate XML outputs in R
https://github.com/quantixed/TrackMateR

Last synced: 28 days ago
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Analysis of TrackMate XML outputs in R

• Host: GitHub
• URL: https://github.com/quantixed/TrackMateR
• Owner: quantixed
• License: other
• Created: 2022-01-30T15:42:44.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-06-07T09:41:30.000Z (6 months ago)
• Last Synced: 2024-11-13T05:09:21.218Z (29 days ago)
• Language: R
• Homepage: https://quantixed.github.io/TrackMateR/
• Size: 19.3 MB
• Stars: 12
• Watchers: 3
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE

Awesome Lists containing this project

• awesome-biological-image-analysis - TrackMateR - R package to analyze cell migration and particle tracking experiments using outputs from TrackMate. (Cell migration and particle tracking)

README

        
---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  message = FALSE

)

```

# TrackMateR 

[![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)

[![DOI](https://zenodo.org/badge/453722113.svg)](https://zenodo.org/badge/latestdoi/453722113)

Analysis of TrackMate XML outputs in R.

[TrackMate](https://imagej.net/plugins/trackmate/) is a single-particle tracking plugin for ImageJ/Fiji.

The standard output from a tracking session is in TrackMate XML format.

The 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.

## Installation

Once you have installed [R](https://cran.rstudio.com) and [RStudio Desktop](https://www.rstudio.com/products/rstudio/download/), you can install TrackMateR using devtools

```{r gh-installation, eval = FALSE}

# install.packages("devtools")

devtools::install_github("quantixed/TrackMateR")

```

## An Example

A basic example is to load one TrackMate XML file, calibrate it (if needed) and analyse it.

```{r example, fig.height = 8, fig.width = 8}

library(ggplot2)

library(TrackMateR)

# an example file is provided, otherwise use file.choose()

xmlPath <- system.file("extdata", "ExampleTrackMateData.xml", package="TrackMateR")

# read the TrackMate XML file into R using

tmObj <- readTrackMateXML(XMLpath = xmlPath)

# Pixel size is actually 0.04 um and original data was 1 pixel, xyscalar = 0.04

tmObj <- correctTrackMateData(dataList = tmObj, xyscalar = 0.04, xyunit = "um")

# generate a report

reportDataset(tmObj)

```

TrackMateR can generate several different types of plot individually using commands or it can make them all automatically and create a report for you.

- For details of how to make individual plots and/or tweak the default parameters, see `vignette("TrackMateR")`

- To see how to compare different datasets, see `vignette("comparison")`

- In order to rescale or recalibrate TrackMate data, see `vignette("recalibration")`

## Credits

- TrackMateR builds on initial work by Julien Godet on [trackR](https://github.com/jgodet/trackR).

- Méghane Sittewelle provided example TrackMate data and helped with testing TrackMateR.

- The Fiji plug-in [TrackMate](https://github.com/trackmate-sc/TrackMate) is developed by Jean-Yves Tinevez.

## Limitations, future development

- TrackMateR is currently written for 2D data. 3D data is read but analysis is currently on the first two dimensions.

- Addition of a dry run option to quickly report what data would be analysed by `compareDatasets()`.

- Addition of number of tracks per frame and more advanced calculation of the density of tracks.