{
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  "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>.",
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  "Date/Publication": "2026-01-12 14:36:25 UTC",
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    "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"
      ]
    },
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      "topics": [
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      ]
    },
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      "title": "Split channels into files and extracts size in microns",
      "topics": [
        "splitchannels.file"
      ]
    },
    {
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      "title": "Split RGB images into channels and pixel size information",
      "topics": [
        "splitchannels.folder"
      ]
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      "title": "Find spots using information from two channels",
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      "title": "Find spots using information from two channels",
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      "title": "Find spots using information from two channels for folder",
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      ]
    },
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      "title": "Test for colors in classes distribution for folders",
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