https://github.com/burgerga/mdftracks

R package for reading and writing MTrackJ Data Format (.mdf) files
https://github.com/burgerga/mdftracks

file-format r tracking

Last synced: 3 months ago
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R package for reading and writing MTrackJ Data Format (.mdf) files

• Host: GitHub
• URL: https://github.com/burgerga/mdftracks
• Owner: burgerga
• License: gpl-3.0
• Created: 2016-11-16T16:01:01.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2024-01-12T10:31:24.000Z (about 1 year ago)
• Last Synced: 2024-09-14T21:51:49.190Z (4 months ago)
• Topics: file-format, r, tracking
• Language: R
• Homepage: https://cran.r-project.org/package=mdftracks
• Size: 85.9 KB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.Rmd
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Citation: CITATION.cff

Awesome Lists containing this project

README

        
---

title: mdftracks

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "README-"

)

```

[![R-CMD-check](https://github.com/burgerga/mdftracks/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/burgerga/mdftracks/actions/workflows/R-CMD-check.yaml)

[![Codecov test coverage](https://codecov.io/gh/burgerga/mdftracks/branch/master/graph/badge.svg)](https://app.codecov.io/gh/burgerga/mdftracks?branch=master)

[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/mdftracks)](https://cran.r-project.org/package=mdftracks)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4692671.svg)](https://doi.org/10.5281/zenodo.4692671)

## Overview

mdftracks reads and writes **[MTrackJ](https://imagescience.org/meijering/software/mtrackj/) Data Files** ([`.mdf`](https://imagescience.org/meijering/software/mtrackj/format/)).

Supports clusters, 2D data, and channel information. If desired, generates

unique track identifiers based on cluster and id data from the `.mdf` file.

## Installation

```{r, eval=F}

install.packages('mdftracks')

```

### Development version

To get a bug fix or to use a feature from the development version, you can install the development version from GitHub.

```{r, eval=F}

# install.packages("remotes")

remotes::install_github("burgerga/mdftracks")

```

## Usage

First load the package with 

```{r}

library(mdftracks)

```

### Reading 3D data

```{r}

mdf.file <- system.file("extdata", "example.mdf", package = 'mdftracks')

data <- read.mdf(mdf.file)

head(data, 10)

```

### Dropping the z-coordinate for 2D data

```{r}

data <- read.mdf(mdf.file, drop.Z = T)

head(data, 10)

```

### Writing data in `(id, t, x, y, z)` format (e.g., from [celltrackR](https://github.com/ingewortel/celltrackR))

```{r}

library('celltrackR')

tracks.df <- as.data.frame(TCells)

```

```{r, collapse=FALSE}

head(tracks.df, 10)

write.mdf(head(tracks.df, 10), pos.columns = c(3,4))

```

### Writing data with cluster, channel, and point information

```{r, collapse=FALSE}

print(mdftracks.example.data)

write.mdf(mdftracks.example.data, cluster.column = 'cl', id.column = 'id',  

          pos.columns = letters[24:26], channel.column = 'ch', 

          point.column = "p")

```

For more information, please consult the package documentation.