{
  "_id": "6a103376acfb0bcc41c98538",
  "Package": "nucim",
  "Title": "Nucleome Imaging Toolbox",
  "Version": "1.0.13",
  "Date": "2026-01-12",
  "Authors@R": "c(person(\"Volker\", \"Schmid\", role = c(\"aut\", \"cre\"),\nemail = \"volker.schmid@lmu.de\"))",
  "biocViews": "",
  "SystemRequirements": "tiff fftw libcurl openssl",
  "Description": "Tools for 4D nucleome imaging. Quantitative analysis of\nthe 3D nuclear landscape recorded with super-resolved\nfluorescence microscopy. See Volker J. Schmid, Marion Cremer,\nThomas Cremer (2017) <doi:10.1016/j.ymeth.2017.03.013>.",
  "License": "GPL-3",
  "URL": "https://bioimaginggroup.github.io/nucim/",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr, R.rsp",
  "BugReports": "https://github.com/bioimaginggroup/nucim/issues",
  "Config/pak/sysreqs": "cmake libfftw3-dev make libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libssl-dev",
  "Repository": "https://bioimaginggroup.r-universe.dev",
  "Date/Publication": "2026-01-12 14:36:25 UTC",
  "RemoteUrl": "https://github.com/bioimaginggroup/nucim",
  "RemoteRef": "HEAD",
  "RemoteSha": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-12 08:15:20 UTC",
    "User": "root"
  },
  "Author": "Volker Schmid [aut, cre]",
  "Maintainer": "Volker Schmid <volker.schmid@lmu.de>",
  "MD5sum": "1c9e61e2bad6820c109cf6ba29318fa7",
  "_user": "bioimaginggroup",
  "_type": "src",
  "_file": "nucim_1.0.13.tar.gz",
  "_fileid": "e4f7c2e7fde34d3106be6a527a5d3a54ea56494f5a2736e6f2737f4c9ab19b6b",
  "_filesize": 212420,
  "_sha256": "e4f7c2e7fde34d3106be6a527a5d3a54ea56494f5a2736e6f2737f4c9ab19b6b",
  "_created": "2026-05-12T08:15:20.000Z",
  "_published": "2026-05-22T10:44:06.969Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77363975597,
      "time": 183,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6939072518"
    },
    {
      "job": 77363975678,
      "time": 181,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6939072042"
    },
    {
      "job": 77363975619,
      "time": 237,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6939075707"
    },
    {
      "job": 77363975616,
      "time": 200,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6939064138"
    },
    {
      "job": 77363975560,
      "time": 213,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6939011962"
    },
    {
      "job": 77363974964,
      "time": 119,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7158618313"
    },
    {
      "job": 77363975603,
      "time": 95,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6939042384"
    },
    {
      "job": 77363975652,
      "time": 106,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6939047367"
    },
    {
      "job": 77363975754,
      "time": 97,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6939043372"
    }
  ],
  "_buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioimaginggroup/nucim",
  "_commit": {
    "id": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
    "author": "Volker Schmid <volker.schmid@lmu.de>",
    "committer": "Volker Schmid <volker.schmid@lmu.de>",
    "message": "nucim 1.0.13 CRAN-SUBMISSION\n",
    "time": 1768228585
  },
  "_maintainer": {
    "name": "Volker Schmid",
    "email": "volker.schmid@lmu.de",
    "login": "volkerschmid",
    "uuid": 11720066
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "EBImage",
      "role": "Depends"
    },
    {
      "package": "bioimagetools",
      "version": ">= 1.1.4",
      "role": "Depends"
    },
    {
      "package": "fields",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "R.rsp",
      "role": "Suggests"
    }
  ],
  "_owner": "bioimaginggroup",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-03",
      "n": 4
    }
  ],
  "_tags": [],
  "_stars": 2,
  "_contributors": [
    {
      "user": "volkerschmid",
      "count": 207,
      "uuid": 11720066
    }
  ],
  "_userbio": {
    "uuid": 23207005,
    "type": "organization",
    "name": "bioimaginggroup"
  },
  "_downloads": {
    "count": 459,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/nucim"
  },
  "_devurl": "https://github.com/bioimaginggroup/nucim",
  "_pkgdown": "https://bioimaginggroup.github.io/nucim/",
  "_searchresults": 7,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/nucim.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/bioimaginggroup/nucim",
  "_realowner": "bioimaginggroup",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.5.3",
      "date": "2016-10-15"
    },
    {
      "version": "1.0.0",
      "date": "2016-12-05"
    },
    {
      "version": "1.0.6",
      "date": "2018-10-09"
    },
    {
      "version": "1.0.9",
      "date": "2020-05-29"
    },
    {
      "version": "1.0.11",
      "date": "2021-06-10"
    },
    {
      "version": "1.0.13",
      "date": "2026-01-12"
    }
  ],
  "_exports": [
    "barplot_with_interval",
    "barplot_with_interval_23",
    "class.neighbours",
    "class.neighbours.folder",
    "classify",
    "classify.folder",
    "classify.single",
    "classify.table",
    "colors.in.classes",
    "colors.in.classes.folder",
    "compute.distance2border",
    "dapimask",
    "dapimask.file",
    "dapimask.folder",
    "find.spots.file",
    "find.spots.folder",
    "heatmap.color",
    "heatmap7",
    "nearestClassDistances.folder",
    "plot_classify.folder",
    "plot_colors.in.classes.folder",
    "plot_nearestClassDistances.folder",
    "splitchannel",
    "splitchannels",
    "splitchannels.file",
    "splitchannels.folder",
    "spots.combined",
    "spots.combined.file",
    "spots.combined.folder",
    "t_colors.in.classes.folder"
  ],
  "_help": [
    {
      "page": "barplot_with_interval",
      "title": "Barplot with Intervals",
      "topics": [
        "barplot_with_interval"
      ]
    },
    {
      "page": "barplot_with_interval_23",
      "title": "Barplot with Intervals for two or three bars beside",
      "topics": [
        "barplot_with_interval_23"
      ]
    },
    {
      "page": "class.neighbours",
      "title": "Class neighbourhood distribution",
      "topics": [
        "class.neighbours"
      ]
    },
    {
      "page": "class.neighbours.folder",
      "title": "class.neighbours.folder",
      "topics": [
        "class.neighbours.folder"
      ]
    },
    {
      "page": "classify",
      "title": "Classify DAPI",
      "topics": [
        "classify"
      ]
    },
    {
      "page": "classify.folder",
      "title": "Classify DAPI",
      "topics": [
        "classify.folder"
      ]
    },
    {
      "page": "classify.single",
      "title": "Classify DAPI",
      "topics": [
        "classify.single"
      ]
    },
    {
      "page": "classify.table",
      "title": "Count classes in classified image",
      "topics": [
        "classify.table"
      ]
    },
    {
      "page": "colors.in.classes",
      "title": "Compute colors in classes distribution",
      "topics": [
        "colors.in.classes"
      ]
    },
    {
      "page": "colors.in.classes.folder",
      "title": "Compute colors in classes distribution for folders",
      "topics": [
        "colors.in.classes.folder"
      ]
    },
    {
      "page": "compute.distance2border",
      "title": "Compute distance to border of classes",
      "topics": [
        "compute.distance2border"
      ]
    },
    {
      "page": "dapimask",
      "title": "Mask DAPI in kernel",
      "topics": [
        "dapimask"
      ]
    },
    {
      "page": "dapimask.file",
      "title": "Automatic DAPI mask segmentation for files",
      "topics": [
        "dapimask.file"
      ]
    },
    {
      "page": "dapimask.folder",
      "title": "Automatic DAPI mask segmentation for folder",
      "topics": [
        "dapimask.folder"
      ]
    },
    {
      "page": "find.spots.file",
      "title": "Detects spots for one file",
      "topics": [
        "find.spots.file"
      ]
    },
    {
      "page": "find.spots.folder",
      "title": "Detects spots",
      "topics": [
        "find.spots.folder"
      ]
    },
    {
      "page": "heatmap.color",
      "title": "Heatmap colors for n classes",
      "topics": [
        "heatmap.color"
      ]
    },
    {
      "page": "heatmap7",
      "title": "Heatmap colors for 7 classes",
      "topics": [
        "heatmap7"
      ]
    },
    {
      "page": "nearestClassDistances.folder",
      "title": "Find all distances to next neighbour of all classes for folders",
      "topics": [
        "nearestClassDistances.folder"
      ]
    },
    {
      "page": "plot_classify.folder",
      "title": "Plot barplot for classified images in a folder",
      "topics": [
        "plot_classify.folder"
      ]
    },
    {
      "page": "plot_colors.in.classes.folder",
      "title": "Plot for colors in classes distribution for folders",
      "topics": [
        "plot_colors.in.classes.folder"
      ]
    },
    {
      "page": "plot_nearestClassDistances.folder",
      "title": "Plots all distances to next neighbour of all classes for folders",
      "topics": [
        "plot_nearestClassDistances.folder"
      ]
    },
    {
      "page": "splitchannel",
      "title": "Split RGB channels",
      "topics": [
        "splitchannel"
      ]
    },
    {
      "page": "splitchannels",
      "title": "Split RGB images into channels and pixel size information",
      "topics": [
        "splitchannels"
      ]
    },
    {
      "page": "splitchannels.file",
      "title": "Split channels into files and extracts size in microns",
      "topics": [
        "splitchannels.file"
      ]
    },
    {
      "page": "splitchannels.folder",
      "title": "Split RGB images into channels and pixel size information",
      "topics": [
        "splitchannels.folder"
      ]
    },
    {
      "page": "spots.combined",
      "title": "Find spots using information from two channels",
      "topics": [
        "spots.combined"
      ]
    },
    {
      "page": "spots.combined.file",
      "title": "Find spots using information from two channels",
      "topics": [
        "spots.combined.file"
      ]
    },
    {
      "page": "spots.combined.folder",
      "title": "Find spots using information from two channels for folder",
      "topics": [
        "spots.combined.folder"
      ]
    },
    {
      "page": "t_colors.in.classes.folder",
      "title": "Test for colors in classes distribution for folders",
      "topics": [
        "t_colors.in.classes.folder"
      ]
    }
  ],
  "_readme": "https://github.com/bioimaginggroup/nucim/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "BiocGenerics",
    "bioimagetools",
    "bitops",
    "bslib",
    "cachem",
    "cli",
    "curl",
    "digest",
    "dotCall64",
    "EBImage",
    "evaluate",
    "fastmap",
    "fftwtools",
    "fields",
    "fontawesome",
    "fs",
    "generics",
    "glue",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "knitr",
    "lattice",
    "lifecycle",
    "locfit",
    "magrittr",
    "maps",
    "memoise",
    "mime",
    "openssl",
    "png",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "rlang",
    "rmarkdown",
    "sass",
    "spam",
    "stringi",
    "stringr",
    "sys",
    "tiff",
    "tinytex",
    "vctrs",
    "viridisLite",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "DAPIclassification.Rmd",
      "filename": "DAPIclassification.html",
      "title": "Chromatin compaction classification using DAPI intensity",
      "author": "Volker Schmid",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Preparation",
        "code to classify one rgb image",
        "code to classify a folder full of rgb images"
      ],
      "created": "2016-11-02 22:59:56",
      "modified": "2020-01-16 14:58:48",
      "commits": 9
    },
    {
      "source": "workflow.html.asis",
      "filename": "workflow.html",
      "title": "Workflow for 3D SIM nucleome analysis",
      "engine": "R.rsp::asis",
      "headings": [],
      "created": "2018-10-08 15:16:11",
      "modified": "2018-10-09 10:46:54",
      "commits": 2
    },
    {
      "source": "workflow_many.Rmd",
      "filename": "workflow_many.html",
      "title": "Workflow on a folder",
      "author": "Volker Schmid",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Preparation",
        "Workflow"
      ],
      "created": "2016-12-08 10:38:28",
      "modified": "2020-01-16 14:58:48",
      "commits": 3
    }
  ],
  "_score": 4.477121254719663,
  "_indexed": true,
  "_nocasepkg": "nucim",
  "_universes": [
    "bioimaginggroup",
    "volkerschmid"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.13",
      "date": "2026-05-12T08:18:12.000Z",
      "distro": "noble",
      "commit": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
      "fileid": "58b87da84caf1494b5788f5bf6b8e4ce00b03cdc5cf9dc94df46beffad8237a5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.13",
      "date": "2026-05-12T08:18:11.000Z",
      "distro": "noble",
      "commit": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
      "fileid": "d2bd9b8a52f8d173a77dc6340a320d96362a2893311dd7799ae7e6928cc4c52a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.0.13",
      "date": "2026-05-12T08:18:27.000Z",
      "commit": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
      "fileid": "d4e29c75435bbfa996455e4c2e4f14ec861475918bc200ec7cba1594eaf906e8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.0.13",
      "date": "2026-05-12T08:17:44.000Z",
      "commit": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
      "fileid": "a388fb92791776b977b620b1a725aeb7cb4eb04fb1f7dae857b960b2b2c8aa87",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.0.13",
      "date": "2026-05-12T08:16:34.000Z",
      "commit": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
      "fileid": "4ac6cca88fa180f514a922923cb653602fc19a524834bbfcc6025e8eac35a7a0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.0.13",
      "date": "2026-05-12T08:16:48.000Z",
      "commit": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
      "fileid": "82b959d598f89bf3dc4b5df138a7832ff728c8995d3c82b00ba64d74ddbd3813",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.0.13",
      "date": "2026-05-12T08:16:34.000Z",
      "commit": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
      "fileid": "4d34a3b431e3292d69b6506e69d8424dfad9886c0e31993dcd07cacb822bbd19",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.0.13",
      "date": "2026-05-22T10:43:48.000Z",
      "commit": "d38c7568f18c6bd683c6ec07f29db3e578ecd531",
      "fileid": "7f1e5882e99587b9ab86d09e68f55c2613050a72f12f3055eeb2a8760554ed34",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioimaginggroup/actions/runs/25722025180"
    }
  ]
}