point_sets_from_tiffs {LOMAR}

point_sets_from_tiffs

Description

Read in single molecule localization events from a series of 3D images in TIFF files where each image file represents a point set.

Usage

point_sets_from_tiffs(
  image_dir = NULL,
  pattern = NULL,
  image.size = NULL,
  sample.size = NULL,
  sample.first = FALSE,
  min.cardinality = NULL,
  max.cardinality = NULL,
  crop.size = NULL
)

Arguments

image_dir

path to a directory containing the TIFF files.

pattern

regular expression, select images whose file path matches the given pattern.

image.size

vector of length 3 containing the size of the images along each dimension, e.g. c(40,40,40).

sample.size

if set, selects this number of images at random. A sample size larger than the available number of samples produces a warning and is ignored.

sample.first

if TRUE, samples are selected before applying any eventual filtering. This is more efficient as it avoids reading all data files.

min.cardinality

if set, filter out all point sets with less than the specified number of points.

max.cardinality

if set, filter out all point sets with more than the specified number of points.

crop.size

vector of length 3 containing the desired reduced size of the images along each dimension, e.g. c(30,30,30).

Value

a list with two elements:

• point.sets: a list of point sets as matrices with columns x,y,z and

• file.names: a vector of paths to the TIFF files from which the point sets were extracted.

Examples

data.dir <- system.file("test_data/img", package = "LOMAR", mustWork = TRUE) 
point_sets <- point_sets_from_tiffs(image_dir = data.dir, pattern = "\\.tiff?$",
 image.size = c(64, 64, 4), min.cardinality = 10)