Tools for Microscopy Imaging


[Up] [Top]

Documentation for package ‘bioimagetools’ version 1.1.5

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