{
  "_id": "6a1b04561d7bb097a0a025bd",
  "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",
  "Encoding": "UTF-8",
  "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",
  "VignetteEngine": "knitr::rmarkdown",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfftw3-dev libfontconfig1-dev\nlibfreetype6-dev make libmagick++-dev gsfonts default-jdk\nlibicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:30 UTC",
  "RemoteUrl": "https://github.com/bioc/SpatialOmicsOverlay",
  "RemoteRef": "HEAD",
  "RemoteSha": "840708e9cbd9284fac0e436380998bae2832f144",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 10:01:25 UTC",
    "User": "root"
  },
  "Author": "Maddy Griswold [cre, aut],\nMegan Vandenberg [ctb],\nStephanie Zimmerman [ctb]",
  "Maintainer": "Maddy Griswold <mgriswold@nanostring.com>",
  "MD5sum": "f41d2cfd9db5d804598d2bad2e71f954",
  "_user": "bioc",
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  "_created": "2026-05-30T10:01:25.000Z",
  "_published": "2026-05-30T15:37:58.307Z",
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676695627",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SpatialOmicsOverlay",
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    "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",
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    "name": "Maddy Griswold",
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    "login": "maddygriz",
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    "uuid": 40255151
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  "_updates": [
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    "transcription",
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    "proprietaryplatforms",
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  "_userbio": {
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 256,
    "source": "https://www.bioconductor.org/packages/stats/bioc/SpatialOmicsOverlay"
  },
  "_searchresults": 21,
  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
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    "extra/readme.md",
    "extra/SpatialOmicsOverlay.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "add4ChannelImage",
    "addImageFile",
    "addImageOmeTiff",
    "addPlottingFactor",
    "bookendStr",
    "changeColoringIntensity",
    "changeImageColoring",
    "checkValidRes",
    "coords",
    "createCoordFile",
    "createMask",
    "cropSamples",
    "cropTissue",
    "downloadMouseBrainImage",
    "flipX",
    "flipY",
    "fluor",
    "fluorLegend",
    "imageInfo",
    "labWork",
    "meta",
    "moveCoords",
    "outline",
    "overlay",
    "parseOverlayAttrs",
    "parseScanMetadata",
    "plotFactors",
    "plotSpatialOverlay",
    "position",
    "readLabWorksheet",
    "readSpatialOverlay",
    "recolor",
    "removeSample",
    "res",
    "sampNames",
    "scaleBarRatio",
    "scaled",
    "scanMeta",
    "seg",
    "show",
    "showImage",
    "slideName",
    "SpatialOverlay",
    "spatialPos",
    "SpatialPosition",
    "workflow",
    "xmlExtraction"
  ],
  "_help": [
    {
      "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",
      "topics": [
        "addImageFile"
      ]
    },
    {
      "page": "addImageOmeTiff",
      "title": "Add image to SpatialOverlay from OME-TIFF",
      "topics": [
        "addImageOmeTiff"
      ]
    },
    {
      "page": "addPlottingFactor",
      "title": "Add plotting factor to 'SpatialOverlay' object",
      "topics": [
        "addPlottingFactor",
        "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": [
        "changeColoringIntensity"
      ]
    },
    {
      "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"
      ]
    },
    {
      "page": "cropSamples",
      "title": "Crop to zoom in on given ROIs",
      "topics": [
        "cropSamples"
      ]
    },
    {
      "page": "cropTissue",
      "title": "Crop to remove black boundary around tissue.",
      "topics": [
        "cropTissue"
      ]
    },
    {
      "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": [
        "flipX"
      ]
    },
    {
      "page": "flipY",
      "title": "Flip y axis in image and overlay points",
      "topics": [
        "flipY"
      ]
    },
    {
      "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": [
        "moveCoords"
      ]
    },
    {
      "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": [
        "readLabWorksheet"
      ]
    },
    {
      "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",
        "plotFactors",
        "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",
        "workflow",
        "workflow,SpatialOverlay-method"
      ]
    },
    {
      "page": "SpatialPosition-class",
      "title": "Class to Contain NanoString Spatial Overlay ROI information",
      "topics": [
        "class:SpatialPosition",
        "meta",
        "meta,SpatialPosition-method",
        "position",
        "position,SpatialPosition-method",
        "show,SpatialPosition-method",
        "spatialPos",
        "spatialPos,SpatialPosition-method",
        "SpatialPosition",
        "SpatialPosition,data.frame-method",
        "SpatialPosition,environment-method",
        "SpatialPosition,matrix-method",
        "SpatialPosition,missing-method",
        "SpatialPosition-class"
      ]
    },
    {
      "page": "xmlExtraction",
      "title": "Extract xml from OME-TIFF",
      "topics": [
        "xmlExtraction"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/SpatialOmicsOverlay/raw/HEAD/README.md",
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      "headers": "openjdk-21-jre-headless",
      "source": "openjdk",
      "version": "21.0.11+10-1~24.04.2",
      "name": "openjdk",
      "homepage": "https://openjdk.java.net/",
      "description": "OpenJDK Java runtime, using Hotspot JIT (headless)"
    }
  ],
  "_vignettes": [
    {
      "source": "SpatialOmicsOverlay.Rmd",
      "filename": "SpatialOmicsOverlay.html",
      "title": "Introduction to SpatialOmicsOverlay",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Load Libraries",
        "Download OME-TIFF from GeoMx",
        "Data Ingestion",
        "SpatialOverlay Accessors",
        "Plotting Without Image",
        "Customizing the graph",
        "Adding the Image",
        "Visualization Marker Legends",
        "Image Manipulation",
        "Flipping Axes",
        "Cropping",
        "Image Coloring",
        "Troubleshooting",
        "java.lang.OutOfMemoryError: Java heap space",
        "java.lang.NegativeArraySizeException",
        "cache resources exhausted",
        "Future Directions"
      ],
      "created": "2022-03-31 22:59:18",
      "modified": "2025-05-12 15:18:54",
      "commits": 21
    }
  ],
  "_score": 4.720159303405957,
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