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  "Package": "SpatialOmicsOverlay",
  "Title": "Spatial Overlay for Omic Data from Nanostring GeoMx Data",
  "Description": "Tools for NanoString Technologies GeoMx Technology.\nPackage to easily graph on top of an OME-TIFF image. Plotting\nannotations can range from tissue segment to gene expression.",
  "Version": "1.13.0",
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  "Authors@R": "c(person(\"Maddy\", \"Griswold\", email = \"mgriswold@nanostring.com\", role = c(\"cre\",\"aut\")),\nperson(\"Megan\", \"Vandenberg\", email = \"mvandenberg@nanostring.com\", role = c(\"ctb\")),\nperson(\"Stephanie\", \"Zimmerman\", role = c(\"ctb\")))",
  "License": "MIT",
  "Collate": "addImage.R addPlottingFactor.R coordinateGeneration.R\nimageManipulation.R omeExtraction.R plottingBasics.R\nreadSpatialOverlay.R removeSamples.R SpatialPosition-class.R\nSpatialOverlay-class.R utils.R xmlParsing.R",
  "biocViews": "GeneExpression, Transcription, CellBasedAssays, DataImport,\nTranscriptomics, Proteomics, ProprietaryPlatforms, RNASeq,\nSpatial, DataRepresentation, Visualization",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:30 UTC",
  "RemoteUrl": "https://github.com/bioc/SpatialOmicsOverlay",
  "RemoteRef": "HEAD",
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  "Author": "Maddy Griswold [cre, aut],\nMegan Vandenberg [ctb],\nStephanie Zimmerman [ctb]",
  "Maintainer": "Maddy Griswold <mgriswold@nanostring.com>",
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  "_expires": "2027-02-09T18:46:57.000Z",
  "_created": "2026-11-01T14:32:07.000Z",
  "_published": "2026-11-01T18:46:58.937Z",
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    "addImageFile",
    "addImageOmeTiff",
    "addPlottingFactor",
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    "changeColoringIntensity",
    "changeImageColoring",
    "checkValidRes",
    "coords",
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    "downloadMouseBrainImage",
    "flipX",
    "flipY",
    "fluor",
    "fluorLegend",
    "imageInfo",
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    "meta",
    "moveCoords",
    "outline",
    "overlay",
    "parseOverlayAttrs",
    "parseScanMetadata",
    "plotFactors",
    "plotSpatialOverlay",
    "position",
    "readLabWorksheet",
    "readSpatialOverlay",
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    "res",
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    "showImage",
    "slideName",
    "SpatialOverlay",
    "spatialPos",
    "SpatialPosition",
    "workflow",
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    {
      "page": "add4ChannelImage",
      "title": "Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of image",
      "topics": [
        "add4ChannelImage"
      ]
    },
    {
      "page": "addImageFile",
      "title": "Add image to SpatialOverlay from disk",
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    {
      "page": "addImageOmeTiff",
      "title": "Add image to SpatialOverlay from OME-TIFF",
      "topics": [
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      ]
    },
    {
      "page": "addPlottingFactor",
      "title": "Add plotting factor to 'SpatialOverlay' object",
      "topics": [
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        "addPlottingFactor,character-method",
        "addPlottingFactor,data.frame-method",
        "addPlottingFactor,factor-method",
        "addPlottingFactor,matrix-method",
        "addPlottingFactor,NanoStringGeoMxSet-method",
        "addPlottingFactor,numeric-method",
        "addPlottingFactor,tbl-method",
        "addPlottingFactor,tbl_df-method"
      ]
    },
    {
      "page": "annotMatching",
      "title": "Match ROIs in annotation file to xml",
      "topics": [
        "annotMatching"
      ]
    },
    {
      "page": "bookendStr",
      "title": "Print long string in more managable fashion",
      "topics": [
        "bookendStr"
      ]
    },
    {
      "page": "changeColoringIntensity",
      "title": "Update color intensities for changing to RGB image",
      "topics": [
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      ]
    },
    {
      "page": "changeImageColoring",
      "title": "Update color scheme for changing to RGB image",
      "topics": [
        "changeImageColoring"
      ]
    },
    {
      "page": "checkValidRes",
      "title": "Determine lowest resolution image in OME-TIFF",
      "topics": [
        "checkValidRes"
      ]
    },
    {
      "page": "createCoordFile",
      "title": "Create coordinate file for entire scan",
      "topics": [
        "createCoordFile"
      ]
    },
    {
      "page": "createMask",
      "title": "Create a binary mask from a base 64 string",
      "topics": [
        "createMask"
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    },
    {
      "page": "cropSamples",
      "title": "Crop to zoom in on given ROIs",
      "topics": [
        "cropSamples"
      ]
    },
    {
      "page": "cropTissue",
      "title": "Crop to remove black boundary around tissue.",
      "topics": [
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    },
    {
      "page": "downloadMouseBrainImage",
      "title": "Download Mouse Brain OME-TIFF from NanoString's Spatial Organ Atlas",
      "topics": [
        "downloadMouseBrainImage"
      ]
    },
    {
      "page": "flipX",
      "title": "Flip x axis in image and overlay points",
      "topics": [
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    },
    {
      "page": "flipY",
      "title": "Flip y axis in image and overlay points",
      "topics": [
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      ]
    },
    {
      "page": "fluorLegend",
      "title": "Add legend of fluorescence targets that make up image",
      "topics": [
        "fluorLegend"
      ]
    },
    {
      "page": "moveCoords",
      "title": "Move coordinates if they don't match image",
      "topics": [
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      ]
    },
    {
      "page": "parseOverlayAttrs",
      "title": "Parse the xml file for AOI attributes in GeoMx images",
      "topics": [
        "parseOverlayAttrs"
      ]
    },
    {
      "page": "parseScanMetadata",
      "title": "Parse the xml file for the scan metadata of GeoMx images",
      "topics": [
        "parseScanMetadata"
      ]
    },
    {
      "page": "plotSpatialOverlay",
      "title": "overlay plots",
      "topics": [
        "plotSpatialOverlay"
      ]
    },
    {
      "page": "readLabWorksheet",
      "title": "Read lab worksheet into dataframe of annotations",
      "topics": [
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    },
    {
      "page": "readSpatialOverlay",
      "title": "Read in 'SpatialOverlay' from tiff file and annotations",
      "topics": [
        "readSpatialOverlay"
      ]
    },
    {
      "page": "recolor",
      "title": "recolor images after changing colors and/or color intensities",
      "topics": [
        "recolor"
      ]
    },
    {
      "page": "removeSample",
      "title": "Remove sample(s) from SpatialOverlay",
      "topics": [
        "removeSample"
      ]
    },
    {
      "page": "SpatialOverlay-class",
      "title": "Class to Contain NanoString Spatial Overlay Images and Data",
      "topics": [
        "class:SpatialOverlay",
        "coords",
        "coords,SpatialOverlay-method",
        "fluor",
        "fluor,SpatialOverlay-method",
        "imageInfo",
        "imageInfo,SpatialOverlay-method",
        "labWork",
        "labWork,SpatialOverlay-method",
        "outline",
        "outline,SpatialOverlay-method",
        "overlay",
        "overlay,SpatialOverlay-method",
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        "plotFactors,SpatialOverlay-method",
        "res",
        "res,SpatialOverlay-method",
        "sampNames",
        "sampNames,SpatialOverlay-method",
        "scaleBarRatio",
        "scaleBarRatio,SpatialOverlay-method",
        "scaled",
        "scaled,SpatialOverlay-method",
        "scanMeta",
        "scanMeta,SpatialOverlay-method",
        "seg",
        "seg,SpatialOverlay-method",
        "show,SpatialOverlay-method",
        "showImage",
        "showImage,SpatialOverlay-method",
        "slideName",
        "slideName,SpatialOverlay-method",
        "SpatialOverlay",
        "SpatialOverlay,character-method",
        "SpatialOverlay-class",
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        "workflow,SpatialOverlay-method"
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      "title": "Class to Contain NanoString Spatial Overlay ROI information",
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        "meta",
        "meta,SpatialPosition-method",
        "position",
        "position,SpatialPosition-method",
        "show,SpatialPosition-method",
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        "spatialPos,SpatialPosition-method",
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        "SpatialPosition,data.frame-method",
        "SpatialPosition,environment-method",
        "SpatialPosition,matrix-method",
        "SpatialPosition,missing-method",
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    },
    {
      "page": "xmlExtraction",
      "title": "Extract xml from OME-TIFF",
      "topics": [
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      ]
    }
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      "filename": "SpatialOmicsOverlay.html",
      "title": "Introduction to SpatialOmicsOverlay",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Load Libraries",
        "Download OME-TIFF from GeoMx",
        "Data Ingestion",
        "SpatialOverlay Accessors",
        "Plotting Without Image",
        "Customizing the graph",
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        "Visualization Marker Legends",
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        "Troubleshooting",
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        "java.lang.NegativeArraySizeException",
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      "modified": "2025-05-12 15:18:54",
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