Nucleome Imaging Toolbox

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Documentation for package ‘nucim’ version 1.0.11

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

barplot_with_interval	Barplot with Intervals
barplot_with_interval_23	Barplot with Intervals for two or three bars beside
class.neighbours	Class neighbourhood distribution
class.neighbours.folder	class.neighbours.folder
classify	Classify DAPI
classify.folder	Classify DAPI
classify.single	Classify DAPI
classify.table	Count classes in classified image
colors.in.classes	Compute colors in classes distribution
colors.in.classes.folder	Compute colors in classes distribution for folders
compute.distance2border	Compute distance to border of classes
dapimask	Mask DAPI in kernel
dapimask.file	Automatic DAPI mask segmentation for files
dapimask.folder	Automatic DAPI mask segmentation for folder
find.spots.file	Detects spots for one file
find.spots.folder	Detects spots
heatmap.color	Heatmap colors for n classes
heatmap7	Heatmap colors for 7 classes
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
splitchannel	Split RGB channels
splitchannels	Split RGB images into channels and pixel size information
splitchannels.file	Split channels into files and extracts size in microns
splitchannels.folder	Split RGB images into channels and pixel size information
spots.combined	Find spots using information from two channels
spots.combined.file	Find spots using information from two channels
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