{
  "_id": "6a17e508acfb0bcc41da0e5a",
  "Package": "cytomapper",
  "Version": "1.25.0",
  "Title": "Visualization of highly multiplexed imaging data in R",
  "Description": "Highly multiplexed imaging acquires the single-cell\nexpression of selected proteins in a spatially-resolved\nfashion. These measurements can be visualised across multiple\nlength-scales. First, pixel-level intensities represent the\nspatial distributions of feature expression with highest\nresolution. Second, after segmentation, expression values or\ncell-level metadata (e.g. cell-type information) can be\nvisualised on segmented cell areas. This package contains\nfunctions for the visualisation of multiplexed read-outs and\ncell-level information obtained by multiplexed imaging\ntechnologies. The main functions of this package allow 1. the\nvisualisation of pixel-level information across multiple\nchannels, 2. the display of cell-level information (expression\nand/or metadata) on segmentation masks and 3. gating and\nvisualisation of single cells.",
  "Authors@R": "c(person(\"Nils\", \"Eling\", role = c(\"aut\"),\nemail = \"nils.eling@dqbm.uzh.ch\",\ncomment = c(ORCID = \"0000-0002-4711-1176\")),\nperson(\"Nicolas\", \"Damond\", role = c(\"aut\"),\nemail = \"nicolas.damond@dqbm.uzh.ch\",\ncomment = c(ORCID = \"0000-0003-3027-8989\")),\nperson(\"Tobias\", \"Hoch\", role = c(\"ctb\")),\nperson(\"Lasse\", \"Meyer\", role = c(\"cre\", \"ctb\"),\nemail = \"lasse.meyer@dqbm.uzh.ch\",\ncomment = c(ORCID = \"0000-0002-1660-1199\")))",
  "License": "GPL (>= 2)",
  "biocViews": "ImmunoOncology, Software, SingleCell, OneChannel,\nTwoChannel, MultipleComparison, Normalization, DataImport",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/BodenmillerGroup/cytomapper",
  "BugReports": "https://github.com/BodenmillerGroup/cytomapper/issues",
  "RoxygenNote": "7.3.1",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "cmake libfftw3-dev libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev make libharfbuzz-dev libmagick++-dev gsfonts\nlibicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev\nlibssl-dev libproj-dev libsqlite3-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:52:15 UTC",
  "RemoteUrl": "https://github.com/bioc/cytomapper",
  "RemoteRef": "HEAD",
  "RemoteSha": "7f3973c8cc632bf33cefe28121b946f468b9ef29",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 06:26:51 UTC",
    "User": "root"
  },
  "Author": "Nils Eling [aut] (ORCID: <https://orcid.org/0000-0002-4711-1176>),\nNicolas Damond [aut] (ORCID: <https://orcid.org/0000-0003-3027-8989>),\nTobias Hoch [ctb],\nLasse Meyer [cre, ctb] (ORCID: <https://orcid.org/0000-0002-1660-1199>)",
  "Maintainer": "Lasse Meyer <lasse.meyer@dqbm.uzh.ch>",
  "MD5sum": "8466907c2c210260d95cba81d58f21e6",
  "_user": "bioc",
  "_type": "src",
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  "_created": "2026-05-28T06:26:51.000Z",
  "_published": "2026-05-28T06:47:36.243Z",
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    "singlecell",
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    "dataimport",
    "bioimaging",
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    "extra/citation.json",
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  "_homeurl": "https://github.com/bodenmillergroup/cytomapper",
  "_realowner": "bioc",
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  "_exports": [
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    "channelNames<-",
    "coerce",
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    "CytoImageList",
    "cytomapperShiny",
    "getChannels",
    "getImages",
    "loadImages",
    "measureObjects",
    "mergeChannels",
    "normalize",
    "plotCells",
    "plotPixels",
    "scaleImages",
    "setChannels<-",
    "setImages<-",
    "show"
  ],
  "_datasets": [
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      "title": "Example CytoImageList object of image files",
      "object": "pancreasImages",
      "file": "pancreasImages.RData",
      "class": [
        "CytoImageList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
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      "title": "Example CytoImageList object of segmentation masks",
      "object": "pancreasMasks",
      "file": "pancreasMasks.RData",
      "class": [
        "CytoImageList"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pancreasSCE",
      "title": "Example SingleCellExperiment object",
      "object": "pancreasSCE",
      "file": "pancreasSCE.RData",
      "class": [
        "SingleCellExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "compImage",
      "title": "Performs channel compensation on multi-channel images",
      "topics": [
        "compImage"
      ]
    },
    {
      "page": "CytoImageList",
      "title": "S4 class for list of images",
      "topics": [
        "coerce,ANY,CytoImageList-method",
        "coerce,list,CytoImageList-method",
        "CytoImageList",
        "CytoImageList-class",
        "show,CytoImageList-method"
      ]
    },
    {
      "page": "CytoImageList-manipulation",
      "title": "Manipulating CytoImageList objects",
      "topics": [
        "CytoImageList-manipulation",
        "normalize",
        "normalize,CytoImageList-method",
        "scaleImages",
        "scaleImages,CytoImageList-method"
      ]
    },
    {
      "page": "CytoImageList-naming",
      "title": "Getting and setting the channel and image names",
      "topics": [
        "channelNames",
        "channelNames,CytoImageList-method",
        "channelNames<-",
        "channelNames<-,CytoImageList-method",
        "CytoImageList-naming",
        "names,CytoImageList-method",
        "names<-,CytoImageList-method"
      ]
    },
    {
      "page": "CytoImageList-subsetting",
      "title": "General subsetting methods for CytoImageList objects",
      "topics": [
        "CytoImageList-subsetting",
        "getChannels",
        "getChannels,CytoImageList-method",
        "getImages",
        "getImages,CytoImageList-method",
        "mergeChannels",
        "setChannels<-",
        "setChannels<-,CytoImageList-method",
        "setImages<-",
        "setImages<-,CytoImageList-method",
        "[<-,CytoImageList,ANY,ANY,CytoImageList-method",
        "[[<-,CytoImageList,ANY,ANY-method"
      ]
    },
    {
      "page": "cytomapperShiny",
      "title": "Shiny application to visualise gated cells on images",
      "topics": [
        "cytomapperShiny"
      ]
    },
    {
      "page": "loadImages",
      "title": "Read images into CytoImageList object",
      "topics": [
        "loadImages"
      ]
    },
    {
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      "title": "Compute morphological and intensity features from objects on images.",
      "topics": [
        "measureObjects"
      ]
    },
    {
      "page": "pancreasImages",
      "title": "Example CytoImageList object of image files",
      "topics": [
        "pancreasImages"
      ]
    },
    {
      "page": "pancreasMasks",
      "title": "Example CytoImageList object of segmentation masks",
      "topics": [
        "pancreasMasks"
      ]
    },
    {
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      "title": "Example SingleCellExperiment object",
      "topics": [
        "pancreasSCE"
      ]
    },
    {
      "page": "plotCells",
      "title": "Function to visualize cell-level information on segmentation masks",
      "topics": [
        "plotCells"
      ]
    },
    {
      "page": "plotPixels",
      "title": "Function to visualize pixel-level information of multi-channel images",
      "topics": [
        "plotPixels"
      ]
    },
    {
      "page": "plotting-param",
      "title": "Further plotting parameters for the cytomapper package",
      "topics": [
        "plotting-param"
      ]
    }
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      "source": "cytomapper_ondisk.Rmd",
      "filename": "cytomapper_ondisk.html",
      "title": "On disk storage and handling of images",
      "author": "Nils Eling",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Reading in data to disk",
        "Converting from on disk to memory and back",
        "Effects on package functionality",
        "Session info",
        "References"
      ],
      "created": "2021-03-20 13:39:54",
      "modified": "2021-04-23 14:25:06",
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    {
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      "filename": "cytomapper.html",
      "title": "Visualization of imaging cytometry data in R",
      "author": "Nils Eling, Nicolas Damond, Tobias Hoch",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Quick start",
        "Data formats",
        "The provided toy dataset",
        "Reading in data",
        "Load images",
        "Add metadata",
        "Scale images",
        "Add channel names",
        "Generating the SingleCellExperiment object",
        "The CytoImageList object",
        "Accessors",
        "Getting and setting images",
        "Getting and setting channels",
        "Naming and merging channels",
        "Looping",
        "Plotting pixel information",
        "Normalization",
        "Colouring",
        "Adjusting brightness, contrast and gamma",
        "Outlining",
        "Subsetting",
        "Adjusting the colour",
        "Plotting cell information",
        "Changing the assay slot",
        "Outlining",
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        "Adjusting the colour",
        "Customisation",
        "Subsetting the SingleCellExperiment object",
        "Background and missing colour",
        "Scale bar and image title",
        "Legend",
        "Setting the margin between images",
        "Scale the feature counts",
        "Image interpolation",
        "Thick borders",
        "Returning plots and images",
        "Integration with ggplot2 objects",
        "Saving images",
        "Gating cells on images",
        "Acknowledgements",
        "Contributions",
        "Session info",
        "References"
      ],
      "created": "2020-05-07 09:50:37",
      "modified": "2021-09-15 15:08:25",
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