Reads one or multiple .txt files into a CytoImageList object

Reader function to generate Image objects in form of a CytoImageList container from .txt files.

readImagefromTXT(
  path,
  pattern = ".txt$",
  channel_pattern = "[A-Za-z]{1,2}[0-9]{2,3}Di",
  index_names = c("X", "Y"),
  BPPARAM = SerialParam()
)

Arguments

path: Full path to where the individual .txt files are located. This is usualy the path where the .mcd file is located.
pattern: pattern to select which files should be read in (default ".txt$").
channel_pattern: regular expression to select the channel names from the files.
index_names: exact names of the columns storing the x and y coordinates of the image
BPPARAM: parameters for parallelized reading in of images. This is only recommended for very large images.

Value

returns a CytoImageList object containing one Image object per .txt file.

Imaging mass cytometry .txt files

As part of the raw data folder, the Hyperion imaging system writes out one .txt file per acquisition. These files store the ion counts per pixel and channel.

This function reads these .txt files into a single CytoImageList object for downstream analysis. The pattern argument allows selection of all .txt files or a specific subset of files. The channelNames of the CytoImageList object are determined by the channel_pattern argument.

Author

Nils Eling (nils.eling@dqbm.uzh.ch)

Examples

path <- system.file("extdata/mockData/raw", package = "imcRtools")

# Read in all images
x <- readImagefromTXT(path)
x
#> CytoImageList containing 3 image(s)
#> names(3): 20210305_NE_mockData2_ROI_001_1 20210305_NE_mockData2_ROI_002_2 20210305_NE_mockData2_ROI_003_3 
#> Each image contains 5 channel(s)
#> channelNames(5): Ag107Di Pr141Di Sm147Di Eu153Di Yb172Di 

# Read in specific files
y <- readImagefromTXT(path, pattern = "ROI_002")
y
#> CytoImageList containing 1 image(s)
#> names(1): 20210305_NE_mockData2_ROI_002_2 
#> Each image contains 5 channel(s)
#> channelNames(5): Ag107Di Pr141Di Sm147Di Eu153Di Yb172Di 

# Read in other channelNames
z <- readImagefromTXT(path, channel_pattern = "[A-Za-z]{2}[0-9]{3}")
z
#> CytoImageList containing 3 image(s)
#> names(3): 20210305_NE_mockData2_ROI_001_1 20210305_NE_mockData2_ROI_002_2 20210305_NE_mockData2_ROI_003_3 
#> Each image contains 5 channel(s)
#> channelNames(5): Ag107 Pr141 Sm147 Eu153 Yb172