Brightness calculations for every image in a folder.

Perform brightness() calculations on all tif images in a folder and save the resulting brightness images to disk.

Usage

brightness_folder(
  folder_path = ".",
  def,
  thresh = NULL,
  detrend = FALSE,
  quick = FALSE,
  filt = NULL,
  s = 1,
  offset = 0,
  readout_noise = 0,
  parallel = FALSE
)

Arguments

folder_path

The path (relative or absolute) to the folder you wish to process.

def

A character. Which definition of brightness do you want to use, "B" or "epsilon"?

thresh

The threshold or thresholding method (see autothresholdr::mean_stack_thresh()) to use on the image prior to detrending and brightness calculations.

detrend

Detrend your data with detrendr::img_detrend_rh(). This is the best known detrending method for brightness analysis. For more fine-grained control over your detrending, use the detrendr package. If there are many channels, this may be specified as a vector, one element for each channel.

quick

If FALSE (the default), the swap finding routine is run several times to get a consensus for the best parameter. If TRUE, the swap finding routine is run only once.

filt

Do you want to smooth (filt = 'mean') or median (filt = 'median') filter the number image using smooth_filter() or median_filter() respectively? If selected, these are invoked here with a filter radius of 1 (with corners included, so each median is the median of 9 elements) and with the option na_count = TRUE. If you want to smooth/median filter the number image in a different way, first calculate the numbers without filtering (filt = NULL) using this function and then perform your desired filtering routine on the result. If there are many channels, this may be specified as a vector, one element for each channel.

s

A positive number. The \(S\)-factor of microscope acquisition.

offset

Microscope acquisition parameters. See reference Dalal et al.

readout_noise

Microscope acquisition parameters. See reference Dalal et al.

parallel

Would you like to use multiple cores to speed up this function? If so, set the number of cores here, or to use all available cores, use parallel = TRUE.

See also

number()

Examples

if (FALSE) { # \dontrun{
setwd(tempdir())
img <- ijtiff::read_tif(system.file("extdata", "50.tif", package = "nandb"))
ijtiff::write_tif(img, "img1.tif")
ijtiff::write_tif(img, "img2.tif")
brightness_folder(def = "B", thresh = "Huang")
} # }