Reference

Main functions
classify()	Classify DAPI
class.neighbours()	Class neighbourhood distribution
colors.in.classes()	Compute colors in classes distribution
compute.distance2border()	Compute distance to border of classes
dapimask()	Mask DAPI in kernel
splitchannel()	Split RGB channels
spots.combined()	Find spots using information from two channels
Functions on folders
classify.folder()	Classify DAPI
class.neighbours.folder()	class.neighbours.folder
colors.in.classes.folder()	Compute colors in classes distribution for folders
dapimask.folder()	Automatic DAPI mask segmentation for folder
find.spots.folder()	Detects spots
nearestClassDistances.folder()	Find all distances to next neighbour of all classes for folders
plot_classify.folder()	Plot barplot for classified images in a folder
plot_colors.in.classes.folder()	Plot for colors in classes distribution for folders
plot_nearestClassDistances.folder()	Plots all distances to next neighbour of all classes for folders
splitchannels.folder()	Split RGB images into channels and pixel size information
spots.combined.folder()	Find spots using information from two channels for folder
t_colors.in.classes.folder()	Test for colors in classes distribution for folders
Plotting
barplot_with_interval_23()	Barplot with Intervals for two or three bars beside
barplot_with_interval()	Barplot with Intervals
heatmap.color()	Heatmap colors for n classes
plot_classify.folder()	Plot barplot for classified images in a folder
plot_colors.in.classes.folder()	Plot for colors in classes distribution for folders
plot_nearestClassDistances.folder()	Plots all distances to next neighbour of all classes for folders
Functions on files
dapimask.file()	Automatic DAPI mask segmentation for files
find.spots.file()	Detects spots for one file
splitchannels.file()	Split channels into files and extracts size in microns
spots.combined.file()	Find spots using information from two channels
Deprecated
classify.single()	Classify DAPI
classify.table()	Count classes in classified image
heatmap7()	Heatmap colors for 7 classes
splitchannels()	Split RGB images into channels and pixel size information