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setRepositories(ind=c(1,2))
install.packages("nucim")
library(bioimagetools)
library(nucim)choose one of the files in a folder of RGB files
folder = folder.choose()scripts can use parallel computing, if available (not under Windows)
nr.cores=ifelse(.Platform$OS.type=="windows", 1, parallel::detectCores())split channels
splitchannels.folder(folder, rgb.folder="./", cores=nr.cores)masks
dapimask.folder(folder, voxelsize=c(0.0395,0.0395,0.125), cores=nr.cores)classification
classify.folder(folder, 7, cores=nr.cores)
plot_classify.folder(folder, 7, cores=nr.cores, col=heatmap7())results will be in folders “class7” and “class7-n”
class distances
nearestClassDistances.folder(folder, voxelsize=c(0.0395,0.0395,0.125), cores=nr.cores)
plot_nearestClassDistances.folder(folder, cores=nr.cores)colors in classes
colors.in.classes.folder(folder, "green", color2="red", cores=nr.cores, thresh1=0.05, thresh2=0.05, type="intensity")
plot_colors.in.classes.folder(folder,"green","red")
t_colors.in.classes.folder(folder,test="wilcox") Works also for contiguous targeted sequences
spots.combined.folder(folder, cores=nr.cores, thresh.offset=0.02, full.voxel=FALSE)
colors.in.classes.folder(folder, "markers_red", color2="markers_green", cores=nr.cores,type="i")
plot_colors.in.classes.folder(folder,"red","green")
t_colors.in.classes.folder(folder,test="wilcox") These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.