Workflow on a folder

Volker Schmid

2021-06-09

Preparation

setRepositories(ind=c(1,2))
install.packages("nucim")
library(bioimagetools)
library(nucim)

Workflow

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")