bioimagetools: Some Tools for Imaging

Tools for 3D imaging, mostly for biology/microscopy. Read and write TIFF stacks. Functions for segmentation, filtering and analysing 3D point patterns.

Author
Volker Schmid [aut, cre], Priyanka Kukreja [ctb], Fabian Scheipl [ctb]
Date of publication
2016-12-01 11:28:44
Maintainer
Volker Schmid <stats@volkerschmid.de>
License
GPL-3
Version
1.0.0
URLs

View on CRAN

Man 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...
filterImage3d
Apply filter to 3D images
folder.choose
Choose a folder interactively
img
image for microscopy
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
nearestClassDistance
Title Find distance to next neighbour of a specific class
nearestClassDistances
Find all distances to next neighbour of all classes
nearest.neighbour.distribution
Nearest neighbour distribution (D curve)
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...
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

Files in this package

bioimagetools
bioimagetools/inst
bioimagetools/inst/extdata
bioimagetools/inst/extdata/cell.csv
bioimagetools/inst/extdata/V.bmp
bioimagetools/inst/extdata/amask.tif
bioimagetools/inst/extdata/kreispunkte.table
bioimagetools/inst/extdata/kringel.tif
bioimagetools/inst/doc
bioimagetools/inst/doc/bioimagetools.html
bioimagetools/inst/doc/bioimagetools.R
bioimagetools/inst/doc/bioimagetools.Rmd
bioimagetools/src
bioimagetools/src/Makevars
bioimagetools/src/getid.c
bioimagetools/src/segment.c
bioimagetools/src/filter.c
bioimagetools/src/Makevars.win
bioimagetools/src/nearestClassDistances.c
bioimagetools/NAMESPACE
bioimagetools/NEWS
bioimagetools/R
bioimagetools/R/bwlabel3d.R
bioimagetools/R/cmoments3d.R
bioimagetools/R/readClassTIF.R
bioimagetools/R/spots.R
bioimagetools/R/writetif.R
bioimagetools/R/cNNTest.R
bioimagetools/R/Kcross3D.R
bioimagetools/R/segment.R
bioimagetools/R/readbmp.R
bioimagetools/R/status.R
bioimagetools/R/readtif.R
bioimagetools/R/folder_choose.R
bioimagetools/R/intensity3d.R
bioimagetools/R/nearestneighbours.R
bioimagetools/R/standardize.R
bioimagetools/R/mexican_hat_brush.R
bioimagetools/R/image.R
bioimagetools/R/nearestclassdistances.R
bioimagetools/R/crossNN.R
bioimagetools/R/onattach.R
bioimagetools/R/nearestneighbourdistribution.R
bioimagetools/R/testColoc.R
bioimagetools/R/tablen.R
bioimagetools/R/plot_nearest_class_distances.R
bioimagetools/R/filterImage3d.R
bioimagetools/R/outside.R
bioimagetools/R/L3cross3d.R
bioimagetools/R/distance2border.R
bioimagetools/R/segmentoutside.R
bioimagetools/vignettes
bioimagetools/vignettes/bioimagetools.Rmd
bioimagetools/README.md
bioimagetools/MD5
bioimagetools/build
bioimagetools/build/vignette.rds
bioimagetools/DESCRIPTION
bioimagetools/man
bioimagetools/man/intensity3D.Rd
bioimagetools/man/mexican.hat.brush.Rd
bioimagetools/man/segment.Rd
bioimagetools/man/writeTIF.Rd
bioimagetools/man/filterImage3d.Rd
bioimagetools/man/crossNN.Rd
bioimagetools/man/folder.choose.Rd
bioimagetools/man/readTIF.Rd
bioimagetools/man/readClassTIF.Rd
bioimagetools/man/bwlabel3d.Rd
bioimagetools/man/K.cross.3D.Rd
bioimagetools/man/spots.Rd
bioimagetools/man/L.cross.3D.Rd
bioimagetools/man/outside.Rd
bioimagetools/man/img.Rd
bioimagetools/man/segment.outside.Rd
bioimagetools/man/nearestClassDistance.Rd
bioimagetools/man/nearest.neighbour.distribution.Rd
bioimagetools/man/testColoc.Rd
bioimagetools/man/cnnTest.Rd
bioimagetools/man/distance2border.Rd
bioimagetools/man/table.n.Rd
bioimagetools/man/cmoments3d.Rd
bioimagetools/man/readBMP.Rd
bioimagetools/man/nearestClassDistances.Rd
bioimagetools/man/plotNearestClassDistances.Rd
bioimagetools/man/standardize.Rd