{"id":17571218,"url":"https://github.com/aoles/rbioformats","last_synced_at":"2026-03-16T22:32:32.046Z","repository":{"id":20641350,"uuid":"23923249","full_name":"aoles/RBioFormats","owner":"aoles","description":":books: R interface to the Bio-Formats library","archived":false,"fork":false,"pushed_at":"2024-05-01T00:14:08.000Z","size":123325,"stargazers_count":25,"open_issues_count":21,"forks_count":14,"subscribers_count":10,"default_branch":"devel","last_synced_at":"2025-03-24T19:22:19.572Z","etag":null,"topics":["bio-formats","bioconductor","image-processing","r"],"latest_commit_sha":null,"homepage":"https://bioconductor.org/packages/RBioFormats","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aoles.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2014-09-11T15:08:23.000Z","updated_at":"2024-12-16T19:26:59.000Z","dependencies_parsed_at":"2024-04-17T08:45:32.513Z","dependency_job_id":"3ad3648a-997c-464b-a300-d705905332b6","html_url":"https://github.com/aoles/RBioFormats","commit_stats":{"total_commits":153,"total_committers":3,"mean_commits":51.0,"dds":"0.013071895424836555","last_synced_commit":"5ec5fad9a5b5ccccc62af638e3c2019f51659816"},"previous_names":[],"tags_count":29,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aoles%2FRBioFormats","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aoles%2FRBioFormats/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aoles%2FRBioFormats/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aoles%2FRBioFormats/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aoles","download_url":"https://codeload.github.com/aoles/RBioFormats/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248311731,"owners_count":21082632,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bio-formats","bioconductor","image-processing","r"],"created_at":"2024-10-21T18:23:03.540Z","updated_at":"2026-03-16T22:32:32.019Z","avatar_url":"https://github.com/aoles.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# R interface to Bio-Formats\n\n*RBioFormats* is an R package which provides an interface to the OME [Bio-Formats](https://github.com/ome/bioformats) Java library. It facilitates reading of proprietary image data and metadata in R.\n\n## Installation\n\nFirst, make sure you have [JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html) 1.8 or higher installed.\nTo install *RBioFormats* use the `biocLite` installation script in order to resolve the dependency on the Bioconductor package *[EBImage](http://biocondcutor.org/packages/EBImage)*.\n\n```r\nif (!require(\"BiocManager\", quietly=TRUE)) install.packages(\"BiocManager\")\nBiocManager::install(\"aoles/RBioFormats\")\n```\n\n### Mac OS X\n\nMac OS comes with a legacy Apple Java 6. In order to use *RBioFormats*, you will need to update your Java installation to a newer version provided by Oracle.\n\n1. Install [Oracle JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html).\n\n2. Update R Java configuration by executing from the command line (you might have to run it as a super user by prepending `sudo` depending on your installation).\n```\nR CMD javareconf\n```\n\n3. Re-install *rJava* from sources in order to properly link to the non-system\nJava installation.\n```r\ninstall.packages(\"rJava\", type=\"source\")\n```\n\nYou can verify your configuration by running the following commands. This should return the Java version string corresponding to the one downloaded and installed in step 1.\n\n```r\nlibrary(rJava)\n.jinit()\n.jcall(\"java/lang/System\", \"S\", \"getProperty\", \"java.runtime.version\")\n## [1] \"1.8.0_112-b16\" \n```\n\n## Documentation\n\nTo get started with using *RBioFormats* have a look at the package vignette.\n\n### FAQ\n\nSee my [answers on Stack Overflow](http://stackoverflow.com/search?q=user:A2792099+rbioformats) for solutions to some common and less common questions.\n\n### Caveats\n\n#### The `java.lang.OutOfMemoryError` error\n\nIf you get the `java.lang.OutOfMemoryError: Java heap space` error, try increasing the maximum heap size by supplying the -Xmx parameter before the Java Virtual Machine is initialized. For example, use\n\n```r\noptions( java.parameters = \"-Xmx4g\" )\nlibrary( \"RBioFormats\" )\n```\n\nto override the default setting and assign 4 gigabytes of heap space to the Java environment.\n\nInformation about the current Java heap space limit can be retrieved by `checkJavaMemory()`.\n\n#### Use with BiocParallel\n\nEach R process needs a separate JVM instance. For this, load the package in the parallelized function, e.g.,\n\n```r\nbplapply (files, function(f) {\n  library(RBioFormats)\n  ...\n})\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faoles%2Frbioformats","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faoles%2Frbioformats","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faoles%2Frbioformats/lists"}