An image in need of detrending
The package contains a sample image series which can be found at
system.file("extdata", "bleached.tif", package = "detrendr"). It’s 500 frames of diffusing fluorescent particles which are bleaching over the course of the acquisition. We can see they’re bleaching by displaying every 99th frame.
library(magrittr)
path <- system.file("extdata", "bleached.tif", package = "detrendr")
img <- ijtiff::read_tif(path, msg = FALSE)
every100th <- purrr::map(seq(1, dim(img)[4], by = 99), ~ img[, , 1, .]) %>%
purrr::reduce(~ cbind(.x, max(img), .y))
ijtiff::display(every100th)
Detrending
We see that the intensity is much lower for the last frame, this is because the image series has been bleached. We can correct for this.
system.time(corrected_exp <- img_detrend_exp(img, "auto", purpose = "FFS",
seed = 0, parallel = 2))["elapsed"]#> elapsed
#> 2.422every100th <- purrr::map(seq(1, dim(img)[4], by = 99),
~ corrected_exp[, , 1, .]) %>%
purrr::reduce(~ cbind(.x, max(img), .y))
ijtiff::display(every100th)
So we see that the corrected series does not have this drop-off in intensity.
Above we used exponential filtering detrending, but we could also use boxcar or polynomial.
system.time(corrected_boxcar <- img_detrend_boxcar(img, "auto", purpose = "FFS",
seed = 0, parallel = 2))["elapsed"]#> elapsed
#> 0.94system.time(corrected_polynom <- img_detrend_polynom(img, "auto",
purpose = "FFS",
seed = 0, parallel = 2))["elapsed"]#> Warning in best_degree(img[, , i, ], seed = seed, parallel = parallel): The
#> polynomial degree found for your detrend was 17. Degrees above 3 are not
#> recommended as they usually indicate eccentric fits. It would be wise to
#> use another detrending method (exponential or boxcar).#> elapsed
#> 4.849Let’s check the mean brightness of each:
#> [1] 1.599681#> [1] 1.449115#> [1] 1.597455So we see that different methods give different results.