{
  "_id": "6a1ad5831d7bb097a09e50cc",
  "Package": "CRImage",
  "Type": "Package",
  "Title": "CRImage a package to classify cells and calculate tumour\ncellularity",
  "Version": "1.61.0",
  "Date": "2012-10-01",
  "Author": "Henrik Failmezger <failmezger@mpipz.mpg.de>, Yinyin Yuan\n<Yinyin.Yuan@cancer.org.uk>, Oscar Rueda\n<oscar.rueda@cancer.org.uk>, Florian Markowetz\n<Florian.Markowetz@cancer.org.uk>",
  "Maintainer": "Henrik Failmezger <failmezger@mpipz.mpg.de>, Yinyin Yuan\n<Yinyin.Yuan@cancer.org.uk>",
  "Description": "CRImage provides functionality to process and analyze\nimages, in particular to classify cells in biological images.\nFurthermore, in the context of tumor images, it provides\nfunctionality to calculate tumour cellularity.",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "Collate": "plotCorrectedCN.R correctCopyNumber.R writeDensityImage.R\nconvertRGBToHSV.R convertHSVToRGB.R imageCompression.R\ncreateBinaryImage.R colorCorrection.R searchStructures.R\nsegmentStructures.R classifyStructures.R numberOfNeighbors.R\nsegmentCytoplasma.R segmentImage.R createClassifier.R\nkernelSmoother.R paintCells.R classifyCells.R\ndetermineCellularity.R calculateCellularity.R findSlices.R\nparseFinalScan.R classificationAperio.R processAperio.R\nPhansalkar_threshold.R SauvolaThreshold.R\ncalculateMeanStdTarget.R convertLABToRGB.R convertRGBToLAB.R\nlocalORThreshold.R oregonThreshold.R localThreshold.R\ncalculateOtsu.R classifyPen.R getImageDistance.R hist3d.R\nlabelCells.R plotImage.R",
  "biocViews": "CellBiology, Classification",
  "Packaged": {
    "Date": "2026-05-30 08:47:27 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "cmake libfftw3-dev make libjpeg-dev libpng-dev\nlibtiff-dev libuv1-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:34:54 UTC",
  "RemoteUrl": "https://github.com/bioc/CRImage",
  "RemoteRef": "HEAD",
  "RemoteSha": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
  "NeedsCompilation": "no",
  "MD5sum": "68599c0871927076c8df73d316b50605",
  "_user": "bioc",
  "_type": "src",
  "_file": "CRImage_1.61.0.tar.gz",
  "_fileid": "505f935ea28940de029b8074ce7904171ebdbbbdb22a5f36e64f15241cb8e52d",
  "_filesize": 8071603,
  "_sha256": "505f935ea28940de029b8074ce7904171ebdbbbdb22a5f36e64f15241cb8e52d",
  "_created": "2026-05-30T08:47:27.000Z",
  "_published": "2026-05-30T12:18:11.868Z",
  "_jobs": [
    {
      "job": 78637565895,
      "time": 160,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306954386"
    },
    {
      "job": 78637565911,
      "time": 217,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306959977"
    },
    {
      "job": 78637565907,
      "time": 197,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306958273"
    },
    {
      "job": 78637565906,
      "time": 111,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7308105725"
    },
    {
      "job": 78637565908,
      "time": 137,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7308108125"
    },
    {
      "job": 78637378144,
      "time": 200,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306938346"
    },
    {
      "job": 78637565903,
      "time": 118,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306950256"
    },
    {
      "job": 78637565910,
      "time": 116,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306950017"
    },
    {
      "job": 78637565914,
      "time": 149,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7306953287"
    },
    {
      "job": 78637565912,
      "time": 137,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306952091"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 19
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/CRImage",
  "_commit": {
    "id": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379694
  },
  "_maintainer": {
    "name": "Henrik Failmezger",
    "email": "yinyin.yuan@cancer.org.uk",
    "login": "treschgroup",
    "description": "",
    "uuid": 3404436
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "EBImage",
      "role": "Depends"
    },
    {
      "package": "DNAcopy",
      "role": "Depends"
    },
    {
      "package": "aCGH",
      "role": "Depends"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "sgeostat",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.61.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.60.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "cellbiology",
    "classification"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 468,
    "source": "https://www.bioconductor.org/packages/stats/bioc/CRImage"
  },
  "_mentions": 5,
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/CRImage.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "calculateCellularity",
    "calculateMeanStdTarget",
    "calculateOtsu",
    "classifyCells",
    "colorCorrection",
    "convertHSVToRGB",
    "convertLABToRGB",
    "convertRGBToHSV",
    "convertRGBToLAB",
    "correctCopyNumber",
    "createBinaryImage",
    "createClassifier",
    "labelCells",
    "plotCorrectedCN",
    "processAperio",
    "SauvolaThreshold",
    "segmentImage"
  ],
  "_help": [
    {
      "page": "CRImage-package",
      "title": "CRImage is a package to analyze images and classify cells.",
      "topics": [
        "CRImage-package",
        "CRImage"
      ]
    },
    {
      "page": "calculateCellularity",
      "title": "Calculation of tumour cellularity",
      "topics": [
        "calculateCellularity"
      ]
    },
    {
      "page": "calculateMeanStdTarget",
      "title": "Calculates Mean and Standard deviation of an image",
      "topics": [
        "calculateMeanStdTarget"
      ]
    },
    {
      "page": "calculateOtsu",
      "title": "Does Otsu thresholding",
      "topics": [
        "calculateOtsu"
      ]
    },
    {
      "page": "classifyCells",
      "title": "A function to classify cells",
      "topics": [
        "classifyCells"
      ]
    },
    {
      "page": "colorCorrection",
      "title": "Color transfer between images.",
      "topics": [
        "colorCorrection"
      ]
    },
    {
      "page": "convertHSVToRGB",
      "title": "Conversion from HSV color space to RGB color space",
      "topics": [
        "convertHSVToRGB"
      ]
    },
    {
      "page": "convertLABToRGB",
      "title": "Conversion of LAB colour space to RGB colour space",
      "topics": [
        "convertLABToRGB"
      ]
    },
    {
      "page": "convertRGBToHSV",
      "title": "Conversion from RGB color space to HSV color space",
      "topics": [
        "convertRGBToHSV"
      ]
    },
    {
      "page": "convertRGBToLAB",
      "title": "Converts RGB to LAB color space.",
      "topics": [
        "convertRGBToLAB"
      ]
    },
    {
      "page": "correctCopyNumber",
      "title": "Allelic Copy Number correction for cellularity",
      "topics": [
        "correctCopyNumber"
      ]
    },
    {
      "page": "createBinaryImage",
      "title": "Thresholding",
      "topics": [
        "createBinaryImage"
      ]
    },
    {
      "page": "createClassifier",
      "title": "Construction of a classifier",
      "topics": [
        "createClassifier"
      ]
    },
    {
      "page": "labelCells",
      "title": "Interactive Session for cell labeling",
      "topics": [
        "labelCells"
      ]
    },
    {
      "page": "plotCorrectedCN",
      "title": "Plot CN profiles corrected for cellularity",
      "topics": [
        "plotCorrectedCN"
      ]
    },
    {
      "page": "processAperio",
      "title": "Cellularity Calculation of Aperio TX Scanner",
      "topics": [
        "processAperio"
      ]
    },
    {
      "page": "SauvolaThreshold",
      "title": "Do Sauvola thresholding",
      "topics": [
        "SauvolaThreshold"
      ]
    },
    {
      "page": "segmentImage",
      "title": "Segmentation of an image",
      "topics": [
        "segmentImage"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "aCGH",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "bitops",
    "bslib",
    "cachem",
    "class",
    "cli",
    "cluster",
    "codetools",
    "digest",
    "DNAcopy",
    "e1071",
    "EBImage",
    "evaluate",
    "fastmap",
    "fftwtools",
    "fontawesome",
    "foreach",
    "fs",
    "generics",
    "highr",
    "htmltools",
    "htmlwidgets",
    "iterators",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "knitr",
    "lattice",
    "lifecycle",
    "locfit",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "multtest",
    "png",
    "proxy",
    "R6",
    "rappdirs",
    "RCurl",
    "rlang",
    "rmarkdown",
    "sass",
    "sgeostat",
    "survival",
    "tiff",
    "tinytex",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "CRImage.Rnw",
      "filename": "CRImage.pdf",
      "title": "CRImage Manual",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 20:15:19",
      "modified": "2013-11-01 20:15:19",
      "commits": 1
    }
  ],
  "_score": 4,
  "_indexed": true,
  "_nocasepkg": "crimage",
  "_universes": [
    "bioc",
    "treschgroup"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.61.0",
      "date": "2026-05-30T08:50:37.000Z",
      "distro": "noble",
      "commit": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
      "fileid": "b3a013aa22a3cca13a87f068b5f963556b6f2d9493ac5123715547969f2cb9c4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.61.0",
      "date": "2026-05-30T08:50:14.000Z",
      "distro": "noble",
      "commit": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
      "fileid": "c7d673028972438ead4e6ffb51994a7f50a602b368f7dc5fe5c90c32e9c9ebe5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.61.0",
      "date": "2026-05-30T12:16:56.000Z",
      "commit": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
      "fileid": "f9c5c4b2255c0f039e553672cfb5ca1c165440c7c91baf77bad68b9f5d5cfeff",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.61.0",
      "date": "2026-05-30T12:17:11.000Z",
      "commit": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
      "fileid": "4f14c37615844e84814df29350220dee2452a317ce20c1a11fdf7859c8c3d947",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.61.0",
      "date": "2026-05-30T08:49:45.000Z",
      "commit": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
      "fileid": "c15253c37d19b2ce22ac072139afbdfd78b2c4398354a11670b04304bf7e9e5d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-05-30T08:48:46.000Z",
      "commit": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
      "fileid": "6cc3df092f6cb6bda3ca84fe4897b96d6074db6ca9e15eea38179a928987586c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-05-30T08:49:18.000Z",
      "commit": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
      "fileid": "ddac8463f01d057c3bebfb372adc29fa09339586ced737afb3d9d9eb90f500b0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.61.0",
      "date": "2026-05-30T08:49:09.000Z",
      "commit": "1d64e666d244f6cab8ae13ba7cc45dde6c8c1424",
      "fileid": "f02d799d2bfebf9f72f1379a7459665ea50ff6f19f77b5882316b3a8d525cbe3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679545415"
    }
  ]
}