detrendr
Detrend Images
Detrend fluorescence microscopy image series for fluorescence
fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This
package contains functionality published in a 2016 paper
Detrend image series.
Installation
To install the release version (recommended) from CRAN, in R, enter
install.packages("detrendr")
To install the development version, in R, first install devtools via install.packages("devtools"). Then enter
devtools::install_github("rorynolan/detrendr")
Use
First let's load the library:
library(detrendr)
Image I/O and display
The package contains a sample image series which can be found at system.file("extdata", "cells.tif", package = "detrendr"). Let's read it in and inspect the first and last frames:
path <- system.file("extdata", "bleached.tif", package = "detrendr")img <- ijtiff::read_tif(path)dim(img) # img has 500 frames
mean(img[, , 1, 1]) # first channel, first frame
#> [1] 152.4489
mean(img[, , 1, 500]) # first channel, last frame
#> [1] 68.51583
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 (and check how long it takes):
system.time(corrected <- img_detrend_exp(img, "auto",seed = 0, parallel = 2))["elapsed"]
#> elapsed
#> 7.589
mean(corrected[, , 1, 1]) # first channel, first frame
#> [1] 112.9569
mean(corrected[, , 1, 500]) # first channel, last frame
#> [1] 103.33
So we see that the corrected series does not have this drop-off in intensity.
Vignette
For more detailed instruction on how to use the package, see vignette("detrendr").
Contribution
Contributions to this package are welcome. The preferred method of contribution is through a github pull request. Feel free to contact me by creating an issue. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
News
detrendr 0.6.1
BUG FIXES
- Require necessary version of
glue. - Temporary fix for upcoming R 3.6 which patches
base::sample(). A more permanent fix should be provided when R 3.6 has landed.
detrendr 0.6.0
NEW FEATURES
- A
pkgdownwebsite!
MINOR IMPROVEMENTS
- Robin Hood parameter finding is now repeated several (at least 9) times to find a sensible consensus value.
- Robin Hood parameter finding includes an adjustment step to avoid over-estimating the number of swaps required.
detrendr 0.5.2
BUG FIXES
- Detrending was not working well for images which had dimension 1 in x or y.
detrendr 0.5.1
BUG FIXES
- Fix tests for CRAN fedora and mac.
detrendr 0.5.0
NEW FEATURES
- The package no longer depends on
RSAGA, making it lighter. - Robin Hood detrending has been added.
detrendr 0.4.0
NEW FEATURES
- Add the option to detrend for the purpose of FCS or FFS.
detrendr 0.3.0
NEW FEATURES
- Batch processing: detrend an entire folder with the likes of
dir_detrend_exp().
BUG FIXES
- Asymmetric images caused R to crash.
NAs in simulated brightnesses were needlessly causing the automatic parameter-finding routines to fail.
detrendr 0.2.0
NEW FEATURES
- The process of extending time series prior to smoothing is not done any more. This was introducing errors for images with low counts. Smoothing works fine without it. Dropping this extension gives a massive improvement in detrending speed :-)
- TIFF I/O and image display are now taken care of by the
ijtiffpackage. - Images are now represented in the style of an
ijtiff::ijtiff_img.
DEFUNCT
- This package no longer exports functions for TIFF I/O nor image display.
detrendr detrendr 0.1.0
- The first CRAN-worthy version.