Description
Usage
Arguments
Note
See Also
Examples
View source: R/number.R
Perform number()
calculations on all tif images in a folder and save the
resulting number images to disk.
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13  (
folder_path = ".",
def,
thresh = ,
detrend = ,
quick = ,
filt = ,
s = 1,
= 0,
readout_noise = 0,
= 1,
=
)

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

def 
A character. Which definition of number do you want to use, "n"
or "N" ?

thresh 
The threshold or thresholding method (see
autothresholdr::mean_stack_thresh() ) to use on the image prior to
detrending and number calculations. If there are many channels, this may be
specified as a vector or list, one element for each channel.

detrend 
Detrend your data with detrendr::img_detrend_rh() . This is
the best known detrending method for brightness analysis. For more
finegrained 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 
FALSE repeats the detrending procedure (which has some inherent
randomness) a few times to hone in on the best detrend. TRUE is quicker,
performing the routine only once. FALSE is better.

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 Sfactor of microscope acquisition.

offset 
Microscope acquisition parameters. See reference
Dalal et al.

readout_noise 
Microscope acquisition parameters. See reference
Dalal et al.

gamma 
Factor for correction of number n due to the illumination
profile. The default (gamma = 1 ) has no effect. Changing gamma will have
the effect of dividing the result by gamma , so the result with gamma = 0.5 is two times the result with gamma = 1 . For a Gaussian illumination
profile, use gamma = 0.3536 ; for a GaussianLorentzian illumination
profile, use gamma = 0.0760 .

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 .

Extreme number values (of magnitude greater than 3.40282e+38) will be
written to the TIFF file as NA
, since TIFF files cannot handle such huge
numbers.
number()
 ## Not run:
(())
img < ijtiff::read_tif(("extdata", "50.tif", package = "nandb"))
ijtiff::write_tif(img, "img2.tif")
(def = "n", thresh = "Huang", = 2)
## End(Not run)

nandb documentation built on May 17, 2021, 1:09 a.m.