Package: bioimagetools 1.1.8

Volker Schmid

bioimagetools: Tools for Microscopy Imaging

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

Authors:Volker Schmid [aut, cre], Priyanka Kukreja [ctb], Fabian Scheipl [ctb]

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bioimagetools.pdf |bioimagetools.html✨
bioimagetools/json (API)
NEWS

# Install 'bioimagetools' in R:

install.packages('bioimagetools', repos = c('https://bioimaginggroup.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioimaginggroup/bioimagetools/issues

Pkgdown site:https://bioimaginggroup.github.io

On CRAN:

biology microscopy

5.30 score 4 stars 1 packages 33 scripts 434 downloads 24 exports 44 dependencies

Last updated 3 years agofrom:65e9a06528. Checks:10 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 22 2025
R-4.5-win-x86_64	OK	Feb 22 2025
R-4.5-mac-x86_64	OK	Feb 22 2025
R-4.5-mac-aarch64	OK	Feb 22 2025
R-4.5-linux-x86_64	OK	Feb 22 2025
R-4.4-win-x86_64	OK	Feb 22 2025
R-4.4-mac-x86_64	OK	Feb 22 2025
R-4.4-mac-aarch64	OK	Feb 22 2025
R-4.3-win-x86_64	OK	Feb 22 2025
R-4.3-mac-x86_64	OK	Feb 22 2025

Exports:bwlabel3d cmoments3d distance2border filterImage3d folder.choose img intensity3D K.cross.3D L.cross.3D mexican.hat.brush nearest.neighbour.distribution nearestClassDistance nearestClassDistances outside plotNearestClassDistances readBMP readClassTIF readTIF segment segment.outside spots standardize table.n writeTIF

Dependencies:abind askpass base64enc BiocGenerics bitops bslib cachem cli curl digest EBImage evaluate fastmap fftwtools fontawesome fs generics glue highr htmltools htmlwidgets httr jpeg jquerylib jsonlite knitr lattice lifecycle locfit memoise mime openssl png R6 rappdirs RCurl rlang rmarkdown sass sys tiff tinytex xfun yaml

Read, write and plot TIFFs

Rendered fromreadwriteplot.html.asisusingR.rsp::asison Feb 22 2025.

Last update: 2022-05-28
Started: 2022-05-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Binary segmentation in 3d	bwlabel3d
Computes moments from image objects	cmoments3d
Permutation Test for cross-type nearest neighbor distances	cnnTest
Compute cross-type nearest neighbor distances	crossNN
A function to compute the distance from spots to borders of classes	distance2border
Apply filter to 3D images	filterImage3d
Choose a folder interactively	folder.choose
Display an image stack	img
Intensity of a 3d Dataset or a Model	intensity3D
K-function cross-type in 3D	K.cross.3D
L-function cross-type in 3d	L.cross.3D
Mexican hat brush to use with filter2	mexican.hat.brush
Nearest neighbor distribution (D curve)	nearest.neighbour.distribution
Title Find distance to next neighbour of a specific class	nearestClassDistance
Find all distances to next neighbor of all classes	nearestClassDistances
Segmentation of the background of 3D images based on classes	outside
Title Plot nearest class distances	plotNearestClassDistances
Read bitmap files	readBMP
Read TIF file with classes	readClassTIF
Read tif stacks	readTIF
Segmentation of 3D images using EM algorithms	segment
Segmentation of the background of 3D images based on automatic threshold	segment.outside
Find spots based on threshold and minimum total intensity	spots
Standardize images	standardize
Cross Tabulation and Table Creation (including empty classes)	table.n
Permutation Test for cross-type nearest neighbor distances	testColoc
Writes image stack into a TIFF file. Wrapper for writeTIFF	writeTIF