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 spotsfor one file

splitchannels.file()

Split channels into files and extracts size in microns

spots.combined.file()

Find spots using information from two channels

Deprectated

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