brightness: Calculate brightness from image series.
In nandb: Number and Brightness Image Analysis

Description Usage Arguments Value References Examples

Given a time stack of images, brightness() performs a calculation of the brightness for each pixel.

brightness(
  img,
  def,
  thresh = NULL,
  detrend = FALSE,
  quick = FALSE,
  filt = NULL,
  s = 1,
  offset = 0,
  readout_noise = 0,
  parallel = FALSE
)

`img`	A 4-dimensional array in the style of an ijtiff_img (indexed by `img[y, x, channel, frame]`) or a 3-dimensional array which is a single channel of an ijtiff_img (indexed by `img[y, x, frame]`).
`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`.

A matrix, the brightness image.

Digman MA, Dalal R, Horwitz AF, Gratton E. Mapping the Number of Molecules and Brightness in the Laser Scanning Microscope. Biophysical Journal. 2008;94(6):2320-2332. doi: 10.1529/biophysj.107.114645.

Dalal, RB, Digman, MA, Horwitz, AF, Vetri, V, Gratton, E (2008). Determination of particle number and brightness using a laser scanning confocal microscope operating in the analog mode. Microsc. Res. Tech., 71, 1:69-81. doi: 10.1002/jemt.20526.

img <- ijtiff::read_tif(system.file("extdata", "50.tif", package = "nandb"))
ijtiff::display(img[, , 1, 1])
b <- brightness(img, "e", thresh = "Huang")
b <- brightness(img, "B", thresh = "tri")