Cross-correlated brightness. — cc

Given a time stack of images and two channels, calculate the cross-correlated brightness of those two channels for each pixel.

cc_brightness(
  img,
  ch1 = 1,
  ch2 = 2,
  thresh = NULL,
  detrend = FALSE,
  quick = FALSE,
  filt = NULL,
  parallel = FALSE
)

Arguments

img	A 4-dimensional array of images indexed by `img[y, x, channel, frame]` (an object of class ijtiff::ijtiff_img). The image to perform the calculation on. To perform this on a file that has not yet been read in, set this argument to the path to that file (a string).
ch1	A natural number. The index of the first channel to use.
ch2	A natural number. The index of the second channel to use.
thresh	Do you want to apply an intensity threshold prior to calculating cross-correlated brightness (via `autothresholdr::mean_stack_thresh()`)? If so, set your thresholding method here. If this is a single value, that same threshold will be applied to both channels. If this is a length-2 vector or list, then these two thresholds will be applied to channels 1 and 2 respectively. A value of `NA` for either channel gives no thresholding for that channel.
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. To detrend one channel and not the other, specify this as a length 2 vector.
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 = 'smooth'`) or median (`filt = 'median'`) filter the cross-correlated brightness image using `smooth_filter()` or `median_filter()` respectively? If selected, these are invoked here with a filter radius of 1 and with the option `na_count = TRUE`. A value of `NA` for either channel gives no thresholding for that channel. If you want to smooth/median filter the cross-correlated brightness image in a different way, first calculate the cross-correlated brightnesses without filtering (`filt = NULL`) using this function and then perform your desired filtering routine on the result.
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`.

Value

A numeric matrix, the cross-correlated brightness image.

Examples

# \donttest{
img <- ijtiff::read_tif(system.file("extdata", "two_ch.tif",
  package = "nandb"
))
#> Reading two_ch.tif: an 8-bit, 30x28 pixel image of unsigned
#> integer type. Reading 2 channels and 100 frames . . .
#>  Done.
ijtiff::display(detrendr::mean_pillars(img[, , 1, ]))
#> Using basic display functionality.
#>   * For better display functionality, install the EBImage package.
#>   * To install `EBImage`:
#>     - Install `BiocManager` with `install.packages("BiocManager")`.
#>     - Then run `BiocManager::install("EBImage")`.
ijtiff::display(detrendr::mean_pillars(img[, , 2, ]))
#> Using basic display functionality.
#>   * For better display functionality, install the EBImage package.
#>   * To install `EBImage`:
#>     - Install `BiocManager` with `install.packages("BiocManager")`.
#>     - Then run `BiocManager::install("EBImage")`.
b <- brightness(img, def = "e", thresh = "Huang", filt = "median")
ijtiff::display(b[, , 1, 1])
#> Using basic display functionality.
#>   * For better display functionality, install the EBImage package.
#>   * To install `EBImage`:
#>     - Install `BiocManager` with `install.packages("BiocManager")`.
#>     - Then run `BiocManager::install("EBImage")`.
ijtiff::display(b[, , 2, 1])
#> Using basic display functionality.
#>   * For better display functionality, install the EBImage package.
#>   * To install `EBImage`:
#>     - Install `BiocManager` with `install.packages("BiocManager")`.
#>     - Then run `BiocManager::install("EBImage")`.
cc_b <- cc_brightness(img, thresh = "Huang")
ijtiff::display(cc_b[, , 1, 1])
#> Using basic display functionality.
#>   * For better display functionality, install the EBImage package.
#>   * To install `EBImage`:
#>     - Install `BiocManager` with `install.packages("BiocManager")`.
#>     - Then run `BiocManager::install("EBImage")`.
# }