# Tools for Microscopy Imaging

## Documentation for package ‘bioimagetools’ version 1.1.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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