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  "Title": "VoltRon for Spatial Omics Data Integration and Analysis",
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  "Maintainer": "Artür Manukyan <artur-man@hotmail.com>",
  "Description": "VoltRon is a spatial omic analysis toolbox for multi-omics\nintegration using spatial image registration. VoltRon is\ncapable of analyzing multiple types and modalities of\nspatially-aware datasets. VoltRon visualizes and analyzes\nregions of interests (ROIs), spots, cells, molecules and event\ntiles.",
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    "Metadata",
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    "resizeImage",
    "SampleMetadata",
    "saveVoltRon",
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    "vrAssayNames",
    "vrAssayParams",
    "vrAssayTypes",
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    "vrCoordinates",
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      "title": "Example MELC Data",
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      "class": [
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      "tojson": false
    },
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      "class": [
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      "tojson": false
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      "object": "visium_data",
      "class": [
        "VoltRon"
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      "tojson": false
    },
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      "title": "Example Xenium Data",
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      "class": [
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      "tojson": false
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      "title": "VoltRon: VoltRon for Spatial Omics Data Integration and Analysis",
      "topics": [
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      ]
    },
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      "page": "addAssay",
      "title": "Add Assay",
      "topics": [
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        "addAssay,VoltRon-method",
        "addAssay,vrMetadata-method"
      ]
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      "page": "addBlockConnectivity",
      "title": "addBlockConnectivity",
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      "title": "addFeature",
      "topics": [
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        "addFeature,VoltRon-method",
        "addFeature,vrAssayV2-method"
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      "title": "addMetadata",
      "topics": [
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      "title": "addSpatialLayer",
      "topics": [
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      "title": "annotateSpatialData",
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      "title": "as.AnnData",
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      "title": "as.VoltRon",
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        "as.VoltRon.Seurat",
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    },
    {
      "page": "combineChannels",
      "title": "combineChannels",
      "topics": [
        "combineChannels",
        "combineChannels,VoltRon-method",
        "combineChannels,vrAssay-method",
        "combineChannels,vrAssayV2-method",
        "combineChannels,vrImage-method",
        "combineChannels,vrSpatial-method"
      ]
    },
    {
      "page": "combineGraphs",
      "title": "combineGraphs",
      "topics": [
        "combineGraphs"
      ]
    },
    {
      "page": "convertAnnDataToVoltRon",
      "title": "convertAnnDataToVoltRon",
      "topics": [
        "convertAnnDataToVoltRon"
      ]
    },
    {
      "page": "demuxVoltRon",
      "title": "demuxVoltRon",
      "topics": [
        "demuxVoltRon"
      ]
    },
    {
      "page": "dummy_cols",
      "title": "Fast creation of dummy variables",
      "topics": [
        "dummy_cols"
      ]
    },
    {
      "page": "fixVoltRon",
      "title": "fixVoltRon",
      "topics": [
        "fixVoltRon"
      ]
    },
    {
      "page": "flipCoordinates",
      "title": "flipCoordinates",
      "topics": [
        "flipCoordinates",
        "flipCoordinates,VoltRon-method",
        "flipCoordinates,vrAssay-method",
        "flipCoordinates,vrAssayV2-method"
      ]
    },
    {
      "page": "formAssay",
      "title": "formAssay",
      "topics": [
        "formAssay"
      ]
    },
    {
      "page": "formImage",
      "title": "formImage",
      "topics": [
        "formImage"
      ]
    },
    {
      "page": "formVoltRon",
      "title": "formVoltRon",
      "topics": [
        "formVoltRon"
      ]
    },
    {
      "page": "FromSegmentToCrop",
      "title": "FromSegmentToCrop",
      "topics": [
        "FromSegmentToCrop"
      ]
    },
    {
      "page": "generateCosMxImage",
      "title": "generateCosMxImage",
      "topics": [
        "generateCosMxImage"
      ]
    },
    {
      "page": "generateGeoJSON",
      "title": "generateGeoJSON",
      "topics": [
        "generateGeoJSON"
      ]
    },
    {
      "page": "generateSegments",
      "title": "generateSegments",
      "topics": [
        "generateSegments"
      ]
    },
    {
      "page": "generateTileData",
      "title": "generateTileData",
      "topics": [
        "generateTileData",
        "generateTileData,VoltRon-method",
        "generateTileData,vrAssay-method",
        "generateTileData,vrAssayV2-method"
      ]
    },
    {
      "page": "generateXeniumImage",
      "title": "generateXeniumImage",
      "topics": [
        "generateXeniumImage"
      ]
    },
    {
      "page": "getBasilisk",
      "title": "get the Python Basilisk environment",
      "topics": [
        "getBasilisk"
      ]
    },
    {
      "page": "getClusters",
      "title": "getClusters",
      "topics": [
        "getClusters"
      ]
    },
    {
      "page": "getDeconvolution",
      "title": "getDeconvolution",
      "topics": [
        "getDeconvolution"
      ]
    },
    {
      "page": "getDiffExp",
      "title": "getDiffExp",
      "topics": [
        "getDiffExp"
      ]
    },
    {
      "page": "getFeatures",
      "title": "getFeatures",
      "topics": [
        "getFeatures",
        "getFeatures,VoltRon-method",
        "getFeatures,vrAssay-method",
        "getFeatures,vrAssayV2-method"
      ]
    },
    {
      "page": "getHotSpotAnalysis",
      "title": "getHotSpotAnalysis",
      "topics": [
        "getHotSpotAnalysis"
      ]
    },
    {
      "page": "getNicheAssay",
      "title": "getNicheAssay",
      "topics": [
        "getNicheAssay"
      ]
    },
    {
      "page": "getOmeTiffChannels",
      "title": "getOmeTiffChannels",
      "topics": [
        "getOmeTiffChannels"
      ]
    },
    {
      "page": "getPCA",
      "title": "getPCA",
      "topics": [
        "getPCA"
      ]
    },
    {
      "page": "getProfileNeighbors",
      "title": "Get profile specific neighbors",
      "topics": [
        "getProfileNeighbors"
      ]
    },
    {
      "page": "getRcppAutomatedRegistration",
      "title": "getRcppAutomatedRegistration",
      "topics": [
        "getRcppAutomatedRegistration"
      ]
    },
    {
      "page": "getRcppManualRegistration",
      "title": "getRcppManualRegistration",
      "topics": [
        "getRcppManualRegistration"
      ]
    },
    {
      "page": "getSpatialNeighbors",
      "title": "Get spatial neighbors",
      "topics": [
        "getSpatialNeighbors"
      ]
    },
    {
      "page": "getUMAP",
      "title": "getUMAP",
      "topics": [
        "getUMAP"
      ]
    },
    {
      "page": "getVariableFeatures",
      "title": "getVariableFeatures",
      "topics": [
        "getVariableFeatures"
      ]
    },
    {
      "page": "import10Xh5",
      "title": "import10Xh5",
      "topics": [
        "import10Xh5"
      ]
    },
    {
      "page": "importCosMx",
      "title": "importCosMx",
      "topics": [
        "importCosMx"
      ]
    },
    {
      "page": "importDBITSeq",
      "title": "importDBITSeq",
      "topics": [
        "importDBITSeq"
      ]
    },
    {
      "page": "importGenePS",
      "title": "importGenePS",
      "topics": [
        "importGenePS"
      ]
    },
    {
      "page": "importGeoMx",
      "title": "importGeoMx",
      "topics": [
        "importGeoMx"
      ]
    },
    {
      "page": "importImageData",
      "title": "importImageData",
      "topics": [
        "importImageData"
      ]
    },
    {
      "page": "importOpenST",
      "title": "importOpenST",
      "topics": [
        "importOpenST"
      ]
    },
    {
      "page": "importPhenoCycler",
      "title": "importPhenoCycler",
      "topics": [
        "importPhenoCycler"
      ]
    },
    {
      "page": "importQuPathIF",
      "title": "importImageData",
      "topics": [
        "importQuPathIF"
      ]
    },
    {
      "page": "importSTOmics",
      "title": "importSTOmics",
      "topics": [
        "importSTOmics"
      ]
    },
    {
      "page": "importVisium",
      "title": "importVisium",
      "topics": [
        "importVisium"
      ]
    },
    {
      "page": "importVisiumHD",
      "title": "importVisiumHD",
      "topics": [
        "importVisiumHD"
      ]
    },
    {
      "page": "importXenium",
      "title": "importXenium",
      "topics": [
        "importXenium"
      ]
    },
    {
      "page": "knn",
      "title": "knn_annoy",
      "topics": [
        "knn_annoy"
      ]
    },
    {
      "page": "loadVoltRon",
      "title": "loadVoltRon",
      "topics": [
        "loadVoltRon"
      ]
    },
    {
      "page": "melc_data",
      "title": "Example MELC Data",
      "topics": [
        "melc_data"
      ]
    },
    {
      "page": "merge",
      "title": "Merging VoltRon objects",
      "topics": [
        "merge",
        "merge,VoltRon,ANY-method"
      ]
    },
    {
      "page": "merge-vrBlock-ANY-method",
      "title": "Merging vrBlock objects",
      "topics": [
        "merge,vrBlock,ANY-method"
      ]
    },
    {
      "page": "merge-vrMetadata-ANY-method",
      "title": "Merging vrMetadata objects",
      "topics": [
        "merge,vrMetadata,ANY-method"
      ]
    },
    {
      "page": "merge-vrSample-ANY-method",
      "title": "Merging vrSample objects",
      "topics": [
        "merge,vrSample,ANY-method"
      ]
    },
    {
      "page": "merged_object",
      "title": "Example Transfer Data",
      "topics": [
        "merged_object"
      ]
    },
    {
      "page": "Metadata",
      "title": "Metadata",
      "topics": [
        "Metadata",
        "Metadata,VoltRon-method",
        "Metadata<-",
        "Metadata<-,VoltRon-method"
      ]
    },
    {
      "page": "modulateImage",
      "title": "modulateImage",
      "topics": [
        "modulateImage",
        "modulateImage,VoltRon-method",
        "modulateImage,vrAssay-method",
        "modulateImage,vrAssayV2-method",
        "modulateImage,vrImage-method",
        "modulateImage,vrSpatial-method"
      ]
    },
    {
      "page": "normalizeData",
      "title": "Normalize Data",
      "topics": [
        "normalizeData",
        "normalizeData,VoltRon-method",
        "normalizeData,vrAssay-method",
        "normalizeData,vrAssayV2-method"
      ]
    },
    {
      "page": "open_zarr",
      "title": "open_zarr",
      "topics": [
        "open_zarr"
      ]
    },
    {
      "page": "registerSpatialData",
      "title": "registerSpatialData",
      "topics": [
        "registerSpatialData"
      ]
    },
    {
      "page": "resizeImage",
      "title": "resizeImage",
      "topics": [
        "resizeImage",
        "resizeImage,VoltRon-method",
        "resizeImage,vrAssay-method",
        "resizeImage,vrAssayV2-method",
        "resizeImage,vrImage-method",
        "resizeImage,vrSpatial-method"
      ]
    },
    {
      "page": "SampleMetadata",
      "title": "SampleMetadata",
      "topics": [
        "SampleMetadata"
      ]
    },
    {
      "page": "saveVoltRon",
      "title": "saveVoltRon",
      "topics": [
        "saveVoltRon"
      ]
    },
    {
      "page": "slotApply",
      "title": "slotApply",
      "topics": [
        "slotApply"
      ]
    },
    {
      "page": "slotToList",
      "title": "slotToList",
      "topics": [
        "slotToList"
      ]
    },
    {
      "page": "subset",
      "title": "Subsetting VoltRon objects",
      "topics": [
        "subset",
        "subset,VoltRon-method"
      ]
    },
    {
      "page": "subset-vrAssay-method",
      "title": "Subsetting vrAssay objects",
      "topics": [
        "subset,vrAssay-method"
      ]
    },
    {
      "page": "subset-vrAssayV2-method",
      "title": "Subsetting vrAssayV2 objects",
      "topics": [
        "subset,vrAssayV2-method"
      ]
    },
    {
      "page": "subset-vrBlock-method",
      "title": "Subsetting vrBlock objects",
      "topics": [
        "subset,vrBlock-method"
      ]
    },
    {
      "page": "subset-vrImage-method",
      "title": "Subsetting vrImage objects",
      "topics": [
        "subset,vrImage-method"
      ]
    },
    {
      "page": "subset-vrLayer-method",
      "title": "Subsetting vrLayer objects",
      "topics": [
        "subset,vrLayer-method"
      ]
    },
    {
      "page": "subset-vrMetadata-method",
      "title": "Subsetting vrMetadata objects",
      "topics": [
        "subset,vrMetadata-method"
      ]
    },
    {
      "page": "subset-vrSample-method",
      "title": "Subsetting vrSample objects",
      "topics": [
        "subset,vrSample-method"
      ]
    },
    {
      "page": "subset-vrSpatial-method",
      "title": "Subsetting vrSpatial objects",
      "topics": [
        "subset,vrSpatial-method"
      ]
    },
    {
      "page": "subsetCoordinates",
      "title": "subsetCoordinates",
      "topics": [
        "subsetCoordinates"
      ]
    },
    {
      "page": "subsetSegments",
      "title": "subsetSegments",
      "topics": [
        "subsetSegments"
      ]
    },
    {
      "page": "transferData",
      "title": "transferData",
      "topics": [
        "transferData"
      ]
    },
    {
      "page": "updateAssay",
      "title": "Update Assay",
      "topics": [
        "updateAssay",
        "updateAssay,VoltRon-method",
        "updateAssay,vrAssay-method",
        "updateAssay,vrAssayV2-method"
      ]
    },
    {
      "page": "visium_data",
      "title": "Example Visium Data",
      "topics": [
        "visium_data"
      ]
    },
    {
      "page": "VoltRon-class",
      "title": "The VoltRon Class",
      "topics": [
        "VoltRon",
        "VoltRon-class"
      ]
    },
    {
      "page": "VoltRon-methods",
      "title": "Methods for VoltRon",
      "concept": [
        "voltron"
      ],
      "topics": [
        "$.VoltRon",
        "$<-.VoltRon",
        ".DollarNames.VoltRon",
        "VoltRon-methods",
        "[[,VoltRon,character,character-method",
        "[[,VoltRon,character,missing-method",
        "[[,VoltRon-methods",
        "[[<-,VoltRon,character,character-method",
        "[[<-,VoltRon,character,missing-method",
        "[[<-,VoltRon-methods"
      ]
    },
    {
      "page": "vrAssay-class",
      "title": "The vrAssay (VoltRon Assay) Class",
      "topics": [
        "vrAssay",
        "vrAssay-class"
      ]
    },
    {
      "page": "vrAssayNames",
      "title": "Get Assay names",
      "topics": [
        "vrAssayNames",
        "vrAssayNames,VoltRon-method",
        "vrAssayNames,vrAssay-method",
        "vrAssayNames,vrAssayV2-method",
        "vrAssayNames,vrMetadata-method",
        "vrAssayNames<-,vrAssay-method",
        "vrAssayNames<-,vrAssayV2-method"
      ]
    },
    {
      "page": "vrAssayParams",
      "title": "Get assay parameters",
      "topics": [
        "vrAssayParams"
      ]
    },
    {
      "page": "vrAssayTypes",
      "title": "Get assay types",
      "topics": [
        "vrAssayTypes",
        "vrAssayTypes,VoltRon-method",
        "vrAssayTypes,vrAssay-method",
        "vrAssayTypes,vrAssayV2-method"
      ]
    },
    {
      "page": "vrAssayV2-class",
      "title": "The vrAssayV2 (VoltRon Assay) Class",
      "topics": [
        "vrAssayV2",
        "vrAssayV2-class"
      ]
    },
    {
      "page": "vrBarPlot",
      "title": "vrBarPlot",
      "topics": [
        "vrBarPlot"
      ]
    },
    {
      "page": "vrBlock-class",
      "title": "The vrBlock (VoltRon Block) Class",
      "topics": [
        "vrBlock",
        "vrBlock-class"
      ]
    },
    {
      "page": "vrCoordinates",
      "title": "vrCoordinates",
      "topics": [
        "vrCoordinates",
        "vrCoordinates,VoltRon-method",
        "vrCoordinates,vrAssay-method",
        "vrCoordinates,vrAssayV2-method",
        "vrCoordinates,vrImage-method",
        "vrCoordinates,vrSpatial-method",
        "vrCoordinates<-",
        "vrCoordinates<-,VoltRon-method",
        "vrCoordinates<-,vrAssay-method",
        "vrCoordinates<-,vrAssayV2-method",
        "vrCoordinates<-,vrImage-method",
        "vrCoordinates<-,vrSpatial-method"
      ]
    },
    {
      "page": "vrData",
      "title": "vrData",
      "topics": [
        "vrData",
        "vrData,VoltRon-method",
        "vrData,vrAssay-method",
        "vrData,vrAssayV2-method"
      ]
    },
    {
      "page": "vrEmbeddingFeaturePlot",
      "title": "vrEmbeddingFeaturePlot",
      "topics": [
        "vrEmbeddingFeaturePlot"
      ]
    },
    {
      "page": "vrEmbeddingNames",
      "title": "Get Embedding names",
      "topics": [
        "vrEmbeddingNames",
        "vrEmbeddingNames,VoltRon-method",
        "vrEmbeddingNames,vrAssay-method",
        "vrEmbeddingNames,vrAssayV2-method"
      ]
    },
    {
      "page": "vrEmbeddingPlot",
      "title": "vrEmbeddingPlot",
      "topics": [
        "vrEmbeddingPlot"
      ]
    },
    {
      "page": "vrEmbeddings",
      "title": "vrEmbeddings",
      "topics": [
        "vrEmbeddings",
        "vrEmbeddings,VoltRon-method",
        "vrEmbeddings,vrAssay-method",
        "vrEmbeddings,vrAssayV2-method",
        "vrEmbeddings<-",
        "vrEmbeddings<-,VoltRon-method",
        "vrEmbeddings<-,vrAssay-method",
        "vrEmbeddings<-,vrAssayV2-method"
      ]
    },
    {
      "page": "vrFeatureData",
      "title": "Feature Data",
      "topics": [
        "vrFeatureData",
        "vrFeatureData,VoltRon-method",
        "vrFeatureData,vrAssay-method",
        "vrFeatureData,vrAssayV2-method",
        "vrFeatureData<-",
        "vrFeatureData<-,VoltRon-method",
        "vrFeatureData<-,vrAssay-method",
        "vrFeatureData<-,vrAssayV2-method"
      ]
    },
    {
      "page": "vrFeatures",
      "title": "vrFeatures",
      "topics": [
        "vrFeatures",
        "vrFeatures,VoltRon-method",
        "vrFeatures,vrAssay-method",
        "vrFeatures,vrAssayV2-method"
      ]
    },
    {
      "page": "vrFeatureTypeNames",
      "title": "vrFeatureTypeNames",
      "topics": [
        "vrFeatureTypeNames",
        "vrFeatureTypeNames,VoltRon-method",
        "vrFeatureTypeNames,vrAssay-method",
        "vrFeatureTypeNames,vrAssayV2-method"
      ]
    },
    {
      "page": "vrGraph",
      "title": "vrGraph",
      "topics": [
        "vrGraph",
        "vrGraph<-"
      ]
    },
    {
      "page": "vrGraphNames",
      "title": "vrGraphNames",
      "topics": [
        "vrGraphNames"
      ]
    },
    {
      "page": "vrHeatmapPlot",
      "title": "HeatmapPlot",
      "topics": [
        "vrHeatmapPlot"
      ]
    },
    {
      "page": "vrImage-class",
      "title": "The vrImage (VoltRon Image) Class",
      "topics": [
        "vrImage",
        "vrImage-class"
      ]
    },
    {
      "page": "vrImageChannelNames",
      "title": "vrImageChannelNames",
      "topics": [
        "vrImageChannelNames",
        "vrImageChannelNames,VoltRon-method",
        "vrImageChannelNames,vrAssay-method",
        "vrImageChannelNames,vrAssayV2-method",
        "vrImageChannelNames,vrImage-method",
        "vrImageChannelNames,vrSpatial-method"
      ]
    },
    {
      "page": "vrImageNames",
      "title": "vrImageNames",
      "topics": [
        "vrImageNames",
        "vrImageNames,VoltRon-method",
        "vrImageNames,vrAssay-method",
        "vrImageNames,vrAssayV2-method"
      ]
    },
    {
      "page": "vrImages",
      "title": "vrImages",
      "topics": [
        "vrImages",
        "vrImages,VoltRon-method",
        "vrImages,vrAssay-method",
        "vrImages,vrAssayV2-method",
        "vrImages,vrImage-method",
        "vrImages,vrSpatial-method",
        "vrImages<-",
        "vrImages<-,vrAssay-method",
        "vrImages<-,vrAssayV2-method",
        "vrImages<-,vrImage-method",
        "vrImages<-,vrSpatial-method"
      ]
    },
    {
      "page": "vrLayer-class",
      "title": "The vrLayer (VoltRon Layer) Class",
      "topics": [
        "vrLayer",
        "vrLayer-class"
      ]
    },
    {
      "page": "vrLayer-methods",
      "title": "Methods for vrLayer objects",
      "concept": [
        "vrlayer"
      ],
      "topics": [
        "vrLayer-methods",
        "[[,vrLayer,character,ANY-method",
        "[[<-,vrLayer,character,ANY-method"
      ]
    },
    {
      "page": "vrMainAssay",
      "title": "Main Assay",
      "topics": [
        "vrMainAssay",
        "vrMainAssay,VoltRon-method",
        "vrMainAssay<-",
        "vrMainAssay<-,VoltRon-method"
      ]
    },
    {
      "page": "vrMainChannel",
      "title": "vrMainChannel",
      "topics": [
        "vrMainChannel",
        "vrMainChannel,vrAssay-method",
        "vrMainChannel,vrAssayV2-method",
        "vrMainChannel,vrImage-method",
        "vrMainChannel,vrSpatial-method",
        "vrMainChannel<-",
        "vrMainChannel<-,vrAssay-method",
        "vrMainChannel<-,vrAssayV2-method",
        "vrMainChannel<-,vrImage-method",
        "vrMainChannel<-,vrSpatial-method"
      ]
    },
    {
      "page": "vrMainFeatureType",
      "title": "vrMainFeatureType",
      "topics": [
        "vrMainFeatureType",
        "vrMainFeatureType,VoltRon-method",
        "vrMainFeatureType,vrAssay-method",
        "vrMainFeatureType,vrAssayV2-method",
        "vrMainFeatureType<-",
        "vrMainFeatureType<-,VoltRon-method",
        "vrMainFeatureType<-,vrAssay-method",
        "vrMainFeatureType<-,vrAssayV2-method"
      ]
    },
    {
      "page": "vrMainImage",
      "title": "vrMainImage",
      "topics": [
        "vrMainImage",
        "vrMainImage,VoltRon-method",
        "vrMainImage,vrAssay-method",
        "vrMainImage,vrAssayV2-method",
        "vrMainImage<-",
        "vrMainImage<-,VoltRon-method",
        "vrMainImage<-,vrAssay-method",
        "vrMainImage<-,vrAssayV2-method"
      ]
    },
    {
      "page": "vrMainSpatial",
      "title": "vrMainSpatial",
      "topics": [
        "vrMainSpatial",
        "vrMainSpatial,VoltRon-method",
        "vrMainSpatial,vrAssay-method",
        "vrMainSpatial,vrAssayV2-method",
        "vrMainSpatial<-",
        "vrMainSpatial<-,VoltRon-method",
        "vrMainSpatial<-,vrAssay-method",
        "vrMainSpatial<-,vrAssayV2-method"
      ]
    },
    {
      "page": "vrMetadata-class",
      "title": "The vrMetadata (VoltRon Metadata) Class",
      "topics": [
        "vrMetadata",
        "vrMetadata-class"
      ]
    },
    {
      "page": "vrNeighbourhoodEnrichment",
      "title": "vrNeighbourhoodEnrichment",
      "topics": [
        "vrNeighbourhoodEnrichment"
      ]
    },
    {
      "page": "vrNeighbourhoodEnrichmentPlot",
      "title": "vrNeighbourhoodEnrichmentPlot",
      "topics": [
        "vrNeighbourhoodEnrichmentPlot"
      ]
    },
    {
      "page": "vrProportionPlot",
      "title": "vrPercentagePlot",
      "topics": [
        "vrProportionPlot"
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      "page": "vrSample-class",
      "title": "The vrSample (VoltRon Sample) Class",
      "topics": [
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        "[[,vrSample,character,ANY-method",
        "[[<-,vrBlock,character,ANY-method",
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        "vrSegments,vrAssayV2-method",
        "vrSegments,vrImage-method",
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