Package: RBioFormats 1.12.0

Andrzej Oleś

RBioFormats: R interface to Bio-Formats

An R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

Authors:Andrzej Oleś [aut, cre], John Lee [ctb]

RBioFormats_1.12.0.tar.gz
RBioFormats_1.12.0.zip(r-4.7)RBioFormats_1.12.0.zip(r-4.6)RBioFormats_1.12.0.zip(r-4.5)
RBioFormats_1.12.0.tgz(r-4.6-any)RBioFormats_1.12.0.tgz(r-4.5-any)
RBioFormats_1.12.0.tar.gz(r-4.7-any)RBioFormats_1.12.0.tar.gz(r-4.6-any)
RBioFormats_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RBioFormats/json (API)

# Install 'RBioFormats' in R:

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

Bug tracker:https://github.com/aoles/rbioformats/issues

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:RBioFormats-1.13.0(bioc 3.24)RBioFormats-1.12.0(bioc 3.23)

dataimport bio-formats bioconductor image-processing openjdk

8.04 score 27 stars 4 packages 113 scripts 676 downloads 23 exports 40 dependencies

Last updated from:efae7d85f7 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	176
linux-devel-x86_64	NOTE	207
source / vignettes	OK	283
linux-release-x86_64	NOTE	245
macos-release-arm64	NOTE	197
macos-oldrel-arm64	NOTE	167
windows-devel	NOTE	130
windows-release	NOTE	148
windows-oldrel	NOTE	128
wasm-release	OK	122

Exports:AnnotatedImage AnnotatedImageList BioFormats.version checkJavaMemory coreMetadata coreMetadata<-dimorder FormatTools globalMetadata globalMetadata<-ImageMetadata ImageMetadataList metadata metadata<-mockFile read.image read.metadata read.omexml seriesCount seriesMetadata seriesMetadata<-show write.image

Dependencies:abind base64enc BiocGenerics bitops bslib cachem cli digest EBImage evaluate fastmap fftwtools fontawesome fs generics highr htmltools htmlwidgets jpeg jquerylib jsonlite knitr lattice lifecycle locfit memoise mime png R6 rappdirs RCurl rJava rlang rmarkdown S4Vectors sass tiff tinytex xfun yaml

RBioFormats: an R interface to the Bio-Formats library

Andrzej Oleś

Rendered fromRBioFormats.Rmdusingknitr::rmarkdownon Jun 12 2026.

Last update: 2024-04-17
Started: 2014-09-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
AnnotatedImage Class	.AnnotatedImage AnnotatedImage AnnotatedImage-class as.Image.AnnotatedImage print.AnnotatedImage show,AnnotatedImage-method
AnnotatedImageList Class	.AnnotatedImageList AnnotatedImageList AnnotatedImageList-class
Java Memory Settings	checkJavaMemory
Metadata Accessors	coreMetadata coreMetadata<- coreMetadata<-,AnnotatedImage-method coreMetadata<-,ImageMetadata-method globalMetadata globalMetadata<- globalMetadata<-,AnnotatedImage-method globalMetadata<-,ImageMetadata-method metadata,AnnotatedImage-method metadata,AnnotatedImageList-method metadata,ANY-method metadata,ImageMetadata-method metadata,ImageMetadataList-method metadata<-,AnnotatedImage-method seriesMetadata seriesMetadata<- seriesMetadata<-,AnnotatedImage-method seriesMetadata<-,ImageMetadata-method
Image Frames Order	dimorder
Bio-Formats FormatTools Class	FormatTools
ImageMetadata and ImageMetadataList Class	.ImageMetadata .ImageMetadataList ImageMetadata ImageMetadata-class ImageMetadataList ImageMetadataList-class print.ImageMetadata print.ImageMetadataList show,ImageMetadata-method show,ImageMetadataList-method
Generate Test Images	mockFile
R Interface to Bio-Formats	BioFormats.version RBioFormats
Read Images	read.image
Read Image Metadata	read.metadata
Read OME-XML Metadata	read.omexml
Number of Image Series	seriesCount seriesCount,AnnotatedImageList-method seriesCount,ANY-method seriesCount,array-method seriesCount,ImageMetadata-method seriesCount,ImageMetadataList-method seriesCount,matrix-method
Write Images	write.image