mdftracks

Overview

mdftracks reads and writes MTrackJ Data Files (.mdf). Supports clusters, 2D data, and channel information. If desired, generates unique track identifiers based on cluster and id data from the .mdf file.

Installation

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.

# install.packages("remotes")
remotes::install_github("burgerga/mdftracks")

Usage

First load the package with

library(mdftracks)

Reading 3D data

mdf.file <- system.file("extdata", "example.mdf", package = 'mdftracks')
data <- read.mdf(mdf.file)
head(data, 10)
#>        cluster id time   x   y z
#> 1.1.1        1  1    1 782  43 1
#> 1.1.2        1  1    2 784  45 1
#> 1.1.3        1  1    3 780  47 1
#> 1.1.4        1  1    4 786  56 1
#> 1.1.5        1  1    5 794  65 1
#> 1.1.6        1  1    6 800  69 1
#> 1.1.7        1  1    7 805  88 1
#> 1.1.8        1  1    8 804 100 1
#> 1.1.9        1  1    9 814 110 1
#> 1.1.10       1  1   10 823 125 1

Dropping the z-coordinate for 2D data

data <- read.mdf(mdf.file, drop.Z = T)
head(data, 10)
#>        cluster id time   x   y
#> 1.1.1        1  1    1 782  43
#> 1.1.2        1  1    2 784  45
#> 1.1.3        1  1    3 780  47
#> 1.1.4        1  1    4 786  56
#> 1.1.5        1  1    5 794  65
#> 1.1.6        1  1    6 800  69
#> 1.1.7        1  1    7 805  88
#> 1.1.8        1  1    8 804 100
#> 1.1.9        1  1    9 814 110
#> 1.1.10       1  1   10 823 125

Writing data in (id, t, x, y, z) format (e.g., from celltrackR)

library('celltrackR')
tracks.df <- as.data.frame(TCells)

head(tracks.df, 10)

#>    id   t       x       y
#> 1   1  48 90.8534 65.3943
#> 2   1  72 89.5923 64.9042
#> 3   1  96 88.6958 67.1125
#> 4   1 120 87.3437 68.2392
#> 5   1 144 86.2740 67.9236
#> 6   1 168 84.0549 68.2502
#> 7   1 192 85.9669 68.5470
#> 8   1 216 86.5280 69.0346
#> 9   1 240 84.6638 69.4034
#> 10  1 264 81.7699 69.9115

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

#> Using the following column mapping:
#> cluster      id    time       x       y       z channel   point 
#>      NA    "id"     "t"     "x"     "y"      NA      NA      NA

#> Converting factor to numeric in columns: id

#> MTrackJ 1.5.1 Data File
#> Assembly 1
#> Cluster 1
#> Track 1
#> Point 1 90.8534 65.3943 1 48 1
#> Point 2 89.5923 64.9042 1 72 1
#> Point 3 88.6958 67.1125 1 96 1
#> Point 4 87.3437 68.2392 1 120 1
#> Point 5 86.274 67.9236 1 144 1
#> Point 6 84.0549 68.2502 1 168 1
#> Point 7 85.9669 68.547 1 192 1
#> Point 8 86.528 69.0346 1 216 1
#> Point 9 84.6638 69.4034 1 240 1
#> Point 10 81.7699 69.9115 1 264 1
#> End of MTrackJ Data File

Writing data with cluster, channel, and point information

print(mdftracks.example.data)

#>    cl id p     x     y    z t ch uid
#> 1   1  1 1 187.1 263.2 27.4 1  2   1
#> 2   1  1 3 309.2 264.4 15.8 2  2   1
#> 3   1  2 1  18.4 438.5 28.1 1  2   2
#> 4   1  2 2 142.9  58.6 28.2 2  2   2
#> 5   1  2 5 290.1 197.5 18.8 3  2   2
#> 6   2  1 1 310.1  15.4  5.8 1  2   3
#> 7   2  2 1  99.1  33.5 22.5 1  2   4
#> 8   2  2 2 220.2 396.0 16.4 2  2   4
#> 9   2  3 1   8.4 305.8 30.2 1  2   5
#> 10  2  3 2  84.7 227.7 21.1 2  2   5

write.mdf(mdftracks.example.data, cluster.column = 'cl', id.column = 'id',  
          pos.columns = letters[24:26], channel.column = 'ch', 
          point.column = "p")

#> Using the following column mapping:
#> cluster      id    time       x       y       z channel   point 
#>    "cl"    "id"    "id"     "x"     "y"     "z"    "ch"     "p"

#> MTrackJ 1.5.1 Data File
#> Assembly 1
#> Cluster 1
#> Track 1
#> Point 1 187.1 263.2 27.4 1 2
#> Point 3 309.2 264.4 15.8 1 2
#> Track 2
#> Point 1 18.4 438.5 28.1 2 2
#> Point 2 142.9 58.6 28.2 2 2
#> Point 5 290.1 197.5 18.8 2 2
#> Cluster 2
#> Track 1
#> Point 1 310.1 15.4 5.8 1 2
#> Track 2
#> Point 1 99.1 33.5 22.5 2 2
#> Point 2 220.2 396 16.4 2 2
#> Track 3
#> Point 1 8.4 305.8 30.2 3 2
#> Point 2 84.7 227.7 21.1 3 2
#> End of MTrackJ Data File

For more information, please consult the package documentation.