Description
Read and Write 'MTrackJ Data Files'.
Description
'MTrackJ' is an 'ImageJ' plugin for motion tracking and analysis (see <https://imagescience.org/meijering/software/mtrackj/>). This package reads and writes 'MTrackJ Data Files' ('.mdf', see <https://imagescience.org/meijering/software/mtrackj/format/>). It supports 2D data and read/writes cluster, point, and channel information. If desired, generates track identifiers that are unique over the clusters. See the project page for more information and examples.
README.md
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.