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