number {nandb} | R Documentation |
Calculate number from image series.
Description
Given a time stack of images, number()
performs a calculation of the number
for each pixel.
Usage
number(
img,
def,
thresh = NULL,
detrend = FALSE,
quick = FALSE,
filt = NULL,
s = 1,
offset = 0,
readout_noise = 0,
gamma = 1,
parallel = FALSE
)
Arguments
img |
A 4-dimensional array of images indexed by |
def |
A character. Which definition of number do you want to use, |
thresh |
The threshold or thresholding method (see
|
detrend |
Detrend your data with |
quick |
|
filt |
Do you want to smooth ( |
s |
A positive number. The |
offset , readout_noise |
Microscope acquisition parameters. See reference Dalal et al. |
gamma |
Factor for correction of number |
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 |
Value
A matrix, the number image.
References
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.
Hur K-H, Macdonald PJ, Berk S, Angert CI, Chen Y, Mueller JD (2014) Quantitative Measurement of Brightness from Living Cells in the Presence of Photodepletion. PLoS ONE 9(5): e97440. doi: 10.1371/journal.pone.0097440.
Examples
img <- ijtiff::read_tif(system.file("extdata", "50.tif", package = "nandb"))
ijtiff::display(img[, , 1, 1])
num <- number(img, "N", thresh = "Huang")
num <- number(img, "n", thresh = "tri")