Tools for Microscopy Imaging

Documentation for package ‘bioimagetools’ version 1.1.8

bwlabel3d	Binary segmentation in 3d
cmoments3d	Computes moments from image objects
cnnTest	Permutation Test for cross-type nearest neighbor distances
crossNN	Compute cross-type nearest neighbor distances
distance2border	A function to compute the distance from spots to borders of classes
filterImage3d	Apply filter to 3D images
folder.choose	Choose a folder interactively
img	Display an image stack
intensity3D	Intensity of a 3d Dataset or a Model
K.cross.3D	K-function cross-type in 3D
L.cross.3D	L-function cross-type in 3d
mexican.hat.brush	Mexican hat brush to use with filter2
nearest.neighbour.distribution	Nearest neighbor distribution (D curve)
nearestClassDistance	Title Find distance to next neighbour of a specific class
nearestClassDistances	Find all distances to next neighbor of all classes
outside	Segmentation of the background of 3D images based on classes
plotNearestClassDistances	Title Plot nearest class distances
readBMP	Read bitmap files
readClassTIF	Read TIF file with classes
readTIF	Read tif stacks
segment	Segmentation of 3D images using EM algorithms
segment.outside	Segmentation of the background of 3D images based on automatic threshold
spots	Find spots based on threshold and minimum total intensity
standardize	Standardize images
table.n	Cross Tabulation and Table Creation (including empty classes)
testColoc	Permutation Test for cross-type nearest neighbor distances
writeTIF	Writes image stack into a TIFF file. Wrapper for writeTIFF