{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "$id": "https://github.com/vitessce/vitessce/#dataset",
    "title": "Vitessce data set",
    "type": "object",
    "definitions": {
      "components": {
        "description": "The layout array defines the views, or components, rendered in the grid.",
        "type": "array",
        "items": {
          "type": "object",
          "additionalProperties": false,
          "required": ["component", "x", "y"],
          "properties": {
            "component": {
              "type": "string",
              "description": "Specify a component using a name defined in the component registry."
            },
            "props": {
              "type": "object",
              "description": "Extra prop values for the component."
            },
            "x": { "type": "integer" },
            "y": { "type": "integer" },
            "w": { "type": "integer" },
            "h": { "type": "integer" },
            "coordinationScopes": {
              "type": "object",
              "description": "Component-level coordination scope mappings define which coordination object values a particular component can read and write, for each coordination type.",
              "additionalProperties": false,
              "required": [],
              "properties": {
                "dataset": { "type": "string" },
                "embeddingType": { "type": "string" },
                "embeddingZoom": { "type": "string" },
                "embeddingRotation": { "type": "string" },
                "embeddingTargetX": { "type": "string" },
                "embeddingTargetY": { "type": "string" },
                "embeddingTargetZ": { "type": "string" },
                "embeddingCellSetPolygonsVisible": { "type": "string" },
                "embeddingCellSetLabelsVisible": { "type": "string" },
                "embeddingCellSetLabelSize": { "type": "string" },
                "embeddingCellRadius": { "type": "string" },
                "spatialZoom": { "type": "string" },
                "spatialRotation": { "type": "string" },
                "spatialTargetX": { "type": "string" },
                "spatialTargetY": { "type": "string" },
                "spatialTargetZ": { "type": "string" },
                "spatialRotationX": { "type": "string" },
                "spatialRotationY": { "type": "string" },
                "spatialRotationZ": { "type": "string" },
                "spatialRotationOrbit": { "type": "string" },
                "spatialOrbitAxis": { "type": "string" },
                "spatialAxisFixed": { "type": "string" },
                "heatmapZoomX": { "type": "string" },
                "heatmapZoomY": { "type": "string" },
                "heatmapTargetX": { "type": "string" },
                "heatmapTargetY": { "type": "string" },
                "cellFilter": { "type": "string" },
                "cellHighlight": { "type": "string" },
                "cellSetSelection": { "type": "string" },
                "cellSetHighlight": { "type": "string" },
                "cellSetColor": { "type": "string" },
                "geneFilter": { "type": "string" },
                "geneHighlight": { "type": "string" },
                "geneSelection": { "type": "string" },
                "geneExpressionTransform": { "type": "string" },
                "geneExpressionColormap": { "type": "string" },
                "geneExpressionColormapRange": { "type": "string" },
                "cellColorEncoding": { "type": "string" },
                "spatialRasterLayers": { "type": "string" },
                "spatialCellsLayer": { "type": "string" },
                "spatialMoleculesLayer": { "type": "string" },
                "spatialNeighborhoodsLayer": { "type": "string" },
                "genomicZoomX": { "type": "string" },
                "genomicZoomY": { "type": "string" },
                "genomicTargetX": { "type": "string" },
                "genomicTargetY": { "type": "string" },
                "additionalCellSets": { "type": "string" },
                "moleculeHighlight": { "type": "string" }
              }
            }
          }
        }
      },
      "annDataCellSets": {
        "type": "array",
        "description": "Array of cell set configuration, following closely the conventions of the tabular schema",
        "items": {
          "type": "object",
          "additionalProperties": false,
          "required": ["groupName", "setName"],
          "properties": {
            "groupName": {
              "type": "string",
              "description": "The display name for the set, like 'Cell Type' or 'Louvain.'"
            },
            "setName": {
              "type": "string",
              "description": "The location in the AnnData store for the set, like 'obs/louvain' or 'obs/celltype.'"
            }
          }
        }
      },
      "annDataCells": {
        "type": "object",
        "description": "The properties of this object are the configuration for how to layout scatterplots and spatial information",
        "minProperties": 1,
        "additionalProperties": false,
        "required": [],
        "properties": {
          "xy": {
            "type": "string",
            "description": "The location in the AnnData store of cell centroids, like 'obsm/X_centroids.'"
          },
          "poly": {
            "type": "string",
            "description": "The location in the AnnData store of cell polygon outlines, like 'obsm/X_polygons.'"
          },
          "factors": {
            "type": "array",
            "description": "List of locations in the AnnData store of cell sets, like 'obs/louvain'",
            "items": {
              "type": "string"
            }
          },
          "mappings": {
            "patternProperties": {
              ".": {
                "type": "object",
                "description": "An object containing key-values for mappings like { UMAP: { key: 'obsm/X_umap', dims: [0, 1] } }.",
                "additionalProperties": false,
                "required": ["key"],
                "properties": {
                  "key": {
                    "type": "string",
                    "description": "Where to look in the AnnData store for this mapping, like 'obsm/X_umap.'"
                  },
                  "dims": {
                    "type": "array",
                    "description": "Which indices of the obsm object to take for a scatterplot, allowing for, for example, different PCs from obsm/X_pca",
                    "minItems": 2,
                    "maxItems": 2,
                    "items": { "type": "number" }
                  }
                }
              }
            }
          }
        }
      },
      "annDataExpressionMatrix": {
        "type": "object",
        "description": "The properties of this object are the configuration for how to fetch the cell x genes matrix",
        "additionalProperties": false,
        "required": ["matrix"],
        "properties": {
          "matrix": {
            "type": "string",
             "description": "The location in the AnnData store of the cell x gene matrix, like 'obsm/hvg_subset.' or 'X'"
          },
          "geneFilter": {
            "type": "string",
             "description": "The location in the AnnData store of a filter for the genes if using a subset of the data, like 'var.highly_variable.' if the matrix comes from 'obsm/hvg_subset.'"
          },
          "matrixGeneFilter": {
            "type": "string",
             "description": "The location in the AnnData store of a filter for the matrix data (used in heatmap and histogram), like 'var.highly_variable.''"
          }
        }
      },
      "requestInit": {
        "type": "object",
        "description": "The properties of this object correspond to the parameters of the JavaScript fetch() function.",
        "additionalProperties": false,
        "required": [],
        "properties": {
          "method": {
            "type": "string"
          },
          "headers": {
            "type": "object"
          },
          "body": {
            "type": "string"
          },
          "mode": {
            "type": "string"
          },
          "credentials": {
            "type": "string"
          },
          "cache": {
            "type": "string"
          },
          "redirect": {
            "type": "string"
          },
          "referrer": {
            "type": "string"
          },
          "integrity": {
            "type": "string"
          }
        }
      },
      "rasterLayer": {
        "description": "The properties of this object are the rendering settings for the raster layer.",
        "additionalProperties": false,
        "required": ["channels", "colormap", "index", "opacity"],
        "properties": {
          "channels": {
            "type": "array",
            "items": {
              "type": "object",
              "additionalProperties": false,
              "required": ["selection"],
              "properties": {
                "color": {
                  "type": "array",
                  "items": { "type": "number" },
                  "description": "The color to use when rendering this channel under the null colormap."
                },
                "selection": {
                  "type": "object",
                  "description": "Determines the channel selection, e.g. some Z and time slice."
                },
                "slider": {
                  "type": "array",
                  "items": { "type": "number" },
                  "description": "Determines the range for color mapping."
                },
                "visible": {
                  "type": "boolean",
                  "description": "Determines whether this channel of the layer will be rendered in the spatial component."
                }
              }
            }
          },
          "colormap": {
            "oneOf": [
              {
                "type": "string",
                "description": "The name of the colormap to use for this layer."
              },
              {
                "type": "null",
                "description": "Use the solid color definitions."
              }
            ]
          },
          "transparentColor": {
            "oneOf": [
              {
                "type": "array",
                "minItems": 3,
                "maxItems": 3,
                "items": { 
                  "type": "number",
                  "description": "One of R G or B (0 - 255)." 
                },
                "description": "Determines the color to be set to opacity 0"
              },
              {
                "type": "null",
                "description": "No selection."
              }
            ]
          },
          "index": {
            "type": "number",
            "description": "The index of the layer among the array of layers available in the image file."
          },
          "opacity": {
            "type": "number"
          },
          "modelMatrix": {
            "oneOf": [
              {
                "type": "array",
                "minItems": 16,
                "maxItems": 16,
                "description": "transformation matrix for this layer"
              },
              {
                "type": "null",
                "description": "Use no transformation."
              }
            ]
          },
          "domainType": {
            "type": "string",
            "enum": ["Full", "Min/Max"],
            "description": "Determines the extent of the channel slider input element in the layer controller."
          },
          "resolution": {
            "type": "number",
            "description": "Resolution of 3D volumetric rendering"
          },
          "xSlice": {
            "oneOf": [
              {
                "type": "array",
                "minItems": 2,
                "maxItems": 2,
                "description": "Slice bounds"
              },
              {
                "type": "null",
                "description": "No slicing"
              }
            ]
          },
          "renderingMode": {
            "type": "string",
             "description": "Rendering mode of 3D volumetric rendering"
          },
          "ySlice": {
            "oneOf": [
              {
                "type": "array",
                "minItems": 2,
                "maxItems": 2,
                "description": "Slice bounds"
              },
              {
                "type": "null",
                "description": "No slicing"
              }
            ]
          },
          "zSlice": {
            "oneOf": [
              {
                "type": "array",
                "minItems": 2,
                "maxItems": 2,
                "description": "Slice bounds"
              },
              {
                "type": "null",
                "description": "No slicing"
              }
            ]
          },
          "type": {
            "type": "string",
            "enum": ["raster", "bitmask"]
          },
          "use3d": {
            "type": "boolean"
          },
          "visible": {
            "type": "boolean",
            "description": "Determines whether this entire layer will be rendered in the spatial component."
          }
        }
      },
      "moleculesLayer": {
        "type": "object",
        "description": "The properties of this object are the rendering settings for the molecules layer.",
        "additionalProperties": false,
        "required": ["visible", "radius", "opacity"],
        "properties": {
          "visible": {
            "type": "boolean"
          },
          "radius": {
            "type": "number"
          },
          "opacity": {
            "type": "number"
          }
        }
      },
      "cellsLayer": {
        "type": "object",
        "description": "The properties of this object are the rendering settings for the cells layer.",
        "additionalProperties": false,
        "required": ["visible", "stroked", "radius", "opacity"],
        "properties": {
          "visible": {
            "type": "boolean"
          },
          "stroked": {
            "type": "boolean"
          },
          "radius": {
            "type": "number"
          },
          "opacity": {
            "type": "number"
          }
        }
      },
      "neighborhoodsLayer": {
        "type": "object",
        "description": "The properties of this object are the rendering settings for the neighborhoods layer.",
        "additionalProperties": false,
        "required": ["visible"],
        "properties": {
          "visible": {
            "type": "boolean"
          }
        }
      },
      "spatialRasterLayers": {
        "type": "array",
        "description": "Array of Spatial Layers",
        "items": {
          "$ref": "#/definitions/rasterLayer"
        }
      }
    },
    "additionalProperties": false,
    "required": ["version", "name", "datasets", "layout", "initStrategy"],
    "properties": {
      "name": { "type": "string" },
      "public": { "type": "boolean" },
      "description": { "type": "string" },
      "datasets": {
        "type": "array",
        "description": "The datasets array defines groups of files, where the files within each dataset reference the same entities (cells, genes, cell sets, etc).",
        "items": {
          "type": "object",
          "additionalProperties": false,
          "required": ["uid", "files"],
          "properties": {
            "uid": { "type": "string" },
            "name": { "type": "string" },
            "description": { "type": "string" },
            "files": {
              "type": "array",
              "items": {
                "type": "object",
                "additionalProperties": false,
                "required": ["type", "fileType"],
                "properties": {
                  "name": { "type": "string" },
                  "type": { "type": "string" },
                  "fileType": { "type": "string" },
                  "url": { "type": "string" },
                  "options": { "oneOf": [{ "$ref": "#/definitions/annDataCellSets" }, { "$ref": "https://github.com/vitessce/vitessce/#raster" }, { "$ref": "#/definitions/annDataCells" }, { "$ref": "#/definitions/annDataExpressionMatrix" }] },
                  "requestInit": { "$ref": "#/definitions/requestInit" }
                }
              }
            }
          }
        }
      },
      "coordinationSpace": {
        "type": "object",
        "description": "The coordination space stores the values for each scope of each coordination object.",
        "additionalProperties": false,
        "required": [],
        "properties": {
          "dataset": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "string" }
            }
          },
          "embeddingZoom": {
            "type": "object",
            "patternProperties": {
              ".": { "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "embeddingRotation": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "embeddingTargetX": {
            "type": "object",
            "patternProperties": {
              ".": { "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "embeddingTargetY": {
            "type": "object",
            "patternProperties": {
              ".":  { "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "embeddingTargetZ": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "embeddingType": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "string" }
            }
          },
          "embeddingCellSetPolygonsVisible": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "boolean" }
            }
          },
          "embeddingCellSetLabelsVisible": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "boolean" }
            }
          },
          "embeddingCellSetLabelSize": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "embeddingCellRadius": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "spatialZoom": {
            "type": "object",
            "patternProperties": {
              ".":  { "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "spatialRotation": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "spatialTargetX": {
            "type": "object",
            "patternProperties": {
              ".":  { "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "spatialTargetY": {
            "type": "object",
            "patternProperties": {
              ".":  { "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "spatialTargetZ": {
            "type": "object",
            "patternProperties": {
              ".":  { "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "spatialRotationX": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "spatialRotationY": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "spatialRotationZ": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
           "spatialRotationOrbit": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
                  },
                  { "type": "number" }
                ]
              }
            }
          },
          "spatialOrbitAxis": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, value will be automatically set. Only useful for 3D viewing."
                  },
                  { "type": "string" }
                ]
              }
            }
          },
          "spatialAxisFixed": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "Whether or not to have a fixed axis for the camera. Only useful for 3D viewing."
                  },
                  { "type": "boolean" }
                ]
              }
            }
          },
          "spatialRasterLayers": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
                  },
                  { "$ref": "#/definitions/spatialRasterLayers" }
                ]
              }
            }
          },
          "spatialCellsLayer": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
                  },
                  { "$ref": "#/definitions/cellsLayer" }
                ]
              }
            }
          },
          "spatialNeighborhoodsLayer": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
                  },
                  { "$ref": "#/definitions/neighborhoodsLayer" }
                ]
              }
            }
          },
          "spatialMoleculesLayer": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided and auto layer initialization is enabled, layers will be automatically initialized."
                  },
                  { "$ref": "#/definitions/moleculesLayer" }
                ]
              }
            }
          },
          "heatmapZoomX": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "heatmapZoomY": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "heatmapTargetX": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "heatmapTargetY": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "cellFilter": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, no cells will be filtered out initially."
                  },
                  { "type": "array", "items": { "type": "string" } }
                ]
              }
            }
          },
          "cellHighlight": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, no cell will be highlighted initially."
                  },
                  { "type": "string" }
                ]
              }
            }
          },
          "cellSetSelection": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided and auto cell set initialization is enabled, cell set selections will be automatically initialized."
                  },
                  { "type": "array" }
                ]
              }
            }
          },
          "cellSetHighlight": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, no cell sets will be highlighted initially."
                  },
                  { "type": "string" }
                ]
              }
            }
          },
          "cellSetColor": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, cell set colors will be automatically initialized."
                  },
                  {
                    "type": "array",
                    "items": {
                      "type": "object",
                      "additionalProperties": false,
                      "required": ["path", "color"],
                      "properties": {
                        "path": {
                          "type": "array",
                          "items": { "type": "string" }
                        },
                        "color": {
                          "type": "array",
                          "items": { "type": "number" }
                        }
                      }
                    }
                  }
                ]
              }
            }
          },
          "cellColorEncoding": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "string" }
            }
          },
          "geneFilter": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, no genes will be filtered out initially."
                  },
                  { "type": "array", "items": { "type": "string" } }
                ]
              }
            }
          },
          "geneHighlight": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, no genes will be highlighted initially."
                  },
                  { "type": "string" }
                ]
              }
            }
          },
          "geneSelection": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null"
                  },
                  { "type": "array", "items": { "type": "string" } }
                ]
              }
            }
          },
          "geneExpressionTransform": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null"
                  },
                  { "type": "string", "pattern": "log1p" }
                ]
              }
            }
          },
          "geneExpressionColormap": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "string" }
            }
          },
          "geneExpressionColormapRange": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "array", "items": { "type": "number" } }
            }
          },
          "genomicZoomX": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "genomicZoomY": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "genomicTargetX": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "genomicTargetY": {
            "type": "object",
            "patternProperties": {
              ".": { "type": "number" }
            }
          },
          "additionalCellSets": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, no cell will be highlighted initially."
                  },
                  {
                    "$ref": "https://github.com/vitessce/vitessce/#cell-sets"
                  }
                ]
              }
            }
          },
          "moleculeHighlight": {
            "type": "object",
            "patternProperties": {
              ".": {
                "oneOf": [
                  {
                    "type": "null",
                    "description": "If null is provided, no molecule will be highlighted initially."
                  },
                  { "type": "string" }
                ]
              }
            }
          }
        }
      },
      "layout": { "$ref": "#/definitions/components" },
      "initStrategy": {
        "type": "string",
        "enum": ["none", "auto"],
        "description": "The initialization strategy determines how missing coordination objects and coordination scope mappings are initially filled in."
      },
      "version": {
        "type": "string",
        "enum": ["1.0.2"],
        "description": "The schema version for the view config."
      }
    }
  }