Function reference • bioimagetools

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

Reference

Basic function for images

Filtering

Segmentation and masking

Nearest Neighours

3D spatial statistics

Misc