bioimagetools: Tools for Microscopy Imaging
Version 1.1.0

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

AuthorVolker Schmid [aut, cre], Priyanka Kukreja [ctb], Fabian Scheipl [ctb]
Date of publication2017-02-18 22:41:07
MaintainerVolker Schmid <stats@volkerschmid.de>
LicenseGPL-3
Version1.1.0
URL https://bioimaginggroup.github.io/bioimagetools
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bioimagetools")

Getting started

README.md
Read, write and plot TIFFs

Popular man pages

distance2border: A function to compute the distance from spots to borders of...
L.cross.3D: L-function cross-type in 3d
nearest.neighbour.distribution: Nearest neighbour distribution (D curve)
readBMP: Read bitmap files
readTIF: Read tif stacks
segment: Segmentation of 3D images using EM algorithms
segment.outside: Segmentation of the background of 3D images based on...
See all...

All man pages Function index File listing

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: 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
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

Functions

Files

TODO
inst
inst/extdata
inst/extdata/cell.csv
inst/extdata/V.bmp
inst/extdata/amask.tif
inst/extdata/kreispunkte.table
inst/extdata/kringel.tif
inst/doc
inst/doc/readwriteplot.Rmd
inst/doc/readwriteplot.html
inst/doc/bioimagetools.Rmd
inst/doc/readwriteplot.R
src
src/Makevars
src/getid.c
src/bioimagetools.h
src/segment.c
src/filter.c
src/Makevars.win
src/init.c
src/nearestClassDistances.c
NAMESPACE
NEWS
R
R/bwlabel3d.R
R/cmoments3d.R
R/readClassTIF.R
R/isline.R
R/spots.R
R/nearestclassdistances_c.R
R/writetif.R
R/findedges.R
R/cNNTest.R
R/Kcross3D.R
R/nearestneighbourenvelope.R
R/segment.R
R/pcfcross3d.R
R/pcfcross3denvelope.R
R/readbmp.R
R/status.R
R/readtif.R
R/computedistances.R
R/folder_choose.R
R/intensity3d.R
R/nearestneighbours.R
R/standardize.R
R/mexican_hat_brush.R
R/Lcross3denvelope.R
R/findmaxline.R
R/image.R
R/point2class.R
R/pcf3d.R
R/nearestclassdistances.R
R/crossNN.R
R/onattach.R
R/nearestneighbourdistribution.R
R/testColoc.R
R/isinstalled.R
R/Kcross3denvelope.R
R/tablen.R
R/plot_nearest_class_distances.R
R/filterImage3d.R
R/outside.R
R/L3cross3d.R
R/distance2border.R
R/segmentoutside.R
vignettes
vignettes/readwriteplot.Rmd
vignettes/readwriteplot_cache
vignettes/readwriteplot_cache/html
vignettes/readwriteplot_cache/html/img_34191bbe93b3e29109be516210e131a9.RData
vignettes/readwriteplot_cache/html/readMBP_ea19e91ac48b85eb315de3103110e182.rdx
vignettes/readwriteplot_cache/html/readclasstif_d956d368d1179aec302990b988ce25f9.rdb
vignettes/readwriteplot_cache/html/readclasstif_d956d368d1179aec302990b988ce25f9.RData
vignettes/readwriteplot_cache/html/__packages
vignettes/readwriteplot_cache/html/loadlibrary_a3224aaf1dba5036e1809275d38b1e3d.RData
vignettes/readwriteplot_cache/html/readMBP_ea19e91ac48b85eb315de3103110e182.RData
vignettes/readwriteplot_cache/html/loadlibrary_a3224aaf1dba5036e1809275d38b1e3d.rdx
vignettes/readwriteplot_cache/html/writetif_9e84b1de62b7720664e1632dfb16fe32.RData
vignettes/readwriteplot_cache/html/img_34191bbe93b3e29109be516210e131a9.rdx
vignettes/readwriteplot_cache/html/img_34191bbe93b3e29109be516210e131a9.rdb
vignettes/readwriteplot_cache/html/readclasstif_d956d368d1179aec302990b988ce25f9.rdx
vignettes/readwriteplot_cache/html/readMBP_ea19e91ac48b85eb315de3103110e182.rdb
vignettes/readwriteplot_cache/html/writetif_9e84b1de62b7720664e1632dfb16fe32.rdb
vignettes/readwriteplot_cache/html/writetif_9e84b1de62b7720664e1632dfb16fe32.rdx
vignettes/readwriteplot_cache/html/loadlibrary_a3224aaf1dba5036e1809275d38b1e3d.rdb
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/intensity3D.Rd
man/mexican.hat.brush.Rd
man/segment.Rd
man/writeTIF.Rd
man/filterImage3d.Rd
man/crossNN.Rd
man/folder.choose.Rd
man/readTIF.Rd
man/readClassTIF.Rd
man/bwlabel3d.Rd
man/K.cross.3D.Rd
man/spots.Rd
man/L.cross.3D.Rd
man/outside.Rd
man/img.Rd
man/segment.outside.Rd
man/nearestClassDistance.Rd
man/nearest.neighbour.distribution.Rd
man/testColoc.Rd
man/cnnTest.Rd
man/distance2border.Rd
man/table.n.Rd
man/cmoments3d.Rd
man/readBMP.Rd
man/nearestClassDistances.Rd
man/plotNearestClassDistances.Rd
man/standardize.Rd
bioimagetools documentation built on May 19, 2017, 11:14 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.