# Generated by roxygen2: do not edit by hand

export("Img<-")
export("ROIPoly<-")
export("annotGeometries<-")
export("annotGeometry<-")
export("annotGeometryNames<-")
export("annotGraph<-")
export("annotGraphNames<-")
export("annotGraphs<-")
export("cellSeg<-")
export("centroids<-")
export("colData<-")
export("colGeometries<-")
export("colGeometry<-")
export("colGeometryNames<-")
export("colGraph<-")
export("colGraphNames<-")
export("colGraphs<-")
export("dimGeometries<-")
export("dimGeometry<-")
export("dimGeometryNames<-")
export("localResult<-")
export("localResultNames<-")
export("localResults<-")
export("nucSeg<-")
export("rowGeometries<-")
export("rowGeometry<-")
export("rowGeometryNames<-")
export("rowGraph<-")
export("rowGraphNames<-")
export("rowGraphs<-")
export("spatialCoords<-")
export("spatialGraph<-")
export("spatialGraphNames<-")
export("spatialGraphs<-")
export("spotPoly<-")
export("tissueBoundary<-")
export("txSpots<-")
export(.check_features)
export(.check_rg)
export(.check_sample_id)
export(.check_tx_file)
export(.check_tx_file_mem)
export(.ext_)
export(.rm_empty_geometries)
export(.symbol2id)
export(.value2df)
export(.warn_symbol_duplicate)
export(BioFormatsImage)
export(ExtImage)
export(ROIPoly)
export(SFEVersion)
export(SpatRasterImage)
export(SpatialFeatureExperiment)
export(addSelectTx)
export(addTxSpots)
export(addTxTech)
export(addVisiumSpotPoly)
export(affine)
export(affineImg)
export(aggBboxes)
export(aggregateTx)
export(aggregateTxTech)
export(annotGeometries)
export(annotGeometry)
export(annotGeometryNames)
export(annotGraph)
export(annotGraphNames)
export(annotGraphs)
export(annotNPred)
export(annotOp)
export(annotPred)
export(annotSummary)
export(bbox)
export(bbox_center)
export(cellSeg)
export(centroids)
export(changeSampleIDs)
export(colData)
export(colFeatureData)
export(colGeometries)
export(colGeometry)
export(colGeometryNames)
export(colGraph)
export(colGraphNames)
export(colGraphs)
export(counts)
export(crop)
export(cropImg)
export(df2sf)
export(dimGeometries)
export(dimGeometry)
export(dimGeometryNames)
export(findDebrisCells)
export(findSpatialNeighbors)
export(findVisiumGraph)
export(findVisiumHDGraph)
export(formatTxSpots)
export(formatTxTech)
export(gdalParquetAvailable)
export(geometryFeatureData)
export(getImg)
export(getParams)
export(getPixelSize)
export(getTechTxFields)
export(getTissueBoundaryConcave)
export(getTissueBoundaryImg)
export(imageIDs)
export(imgData)
export(imgRaster)
export(imgSource)
export(isFull)
export(localResult)
export(localResultAttrs)
export(localResultFeatures)
export(localResultNames)
export(localResults)
export(logcounts)
export(mirror)
export(mirrorImg)
export(multi_listw2sparse)
export(nucSeg)
export(origin)
export(read10xVisiumSFE)
export(readCosMX)
export(readSelectTx)
export(readVisiumHD)
export(readVizgen)
export(readXenium)
export(reducedDim)
export(reducedDimFeatureData)
export(removeEmptySpace)
export(rmvImg)
export(rotate)
export(rotateImg)
export(rotateMinRect)
export(rowData)
export(rowFeatureData)
export(rowGeometries)
export(rowGeometry)
export(rowGeometryNames)
export(rowGraph)
export(rowGraphNames)
export(rowGraphs)
export(sampleIDs)
export(scale)
export(scaleImg)
export(spatialCoords)
export(spatialCoordsNames)
export(spatialGraph)
export(spatialGraphNames)
export(spatialGraphs)
export(splitByCol)
export(splitComponent)
export(splitContiguity)
export(splitSamples)
export(spotPoly)
export(st_any_intersects)
export(st_any_pred)
export(st_n_intersects)
export(st_n_pred)
export(tissueBoundary)
export(toExtImage)
export(toSpatRasterImage)
export(toSpatialFeatureExperiment)
export(transformation)
export(translate)
export(translateImg)
export(transpose)
export(transposeImg)
export(txSpots)
export(unit)
exportClasses(AlignedSpatialImage)
exportClasses(BioFormatsImage)
exportClasses(ExtImage)
exportClasses(SpatRasterImage)
exportClasses(SpatialFeatureExperiment)
exportMethods("Img<-")
exportMethods("[")
exportMethods("annotGeometries<-")
exportMethods("annotGeometry<-")
exportMethods("annotGeometryNames<-")
exportMethods("dimGeometries<-")
exportMethods("dimGeometry<-")
exportMethods("dimGeometryNames<-")
exportMethods("ext<-")
exportMethods("localResult<-")
exportMethods("localResultNames<-")
exportMethods("localResults<-")
exportMethods("spatialGraph<-")
exportMethods("spatialGraphNames<-")
exportMethods("spatialGraphs<-")
exportMethods(addImg)
exportMethods(affineImg)
exportMethods(aggregate)
exportMethods(annotGeometries)
exportMethods(annotGeometry)
exportMethods(annotGeometryNames)
exportMethods(bbox)
exportMethods(cbind)
exportMethods(cropImg)
exportMethods(dim)
exportMethods(dimGeometries)
exportMethods(dimGeometry)
exportMethods(dimGeometryNames)
exportMethods(ext)
exportMethods(findDebrisCells)
exportMethods(findSpatialNeighbors)
exportMethods(getTissueBoundaryConcave)
exportMethods(imgRaster)
exportMethods(imgSource)
exportMethods(isFull)
exportMethods(localResult)
exportMethods(localResultAttrs)
exportMethods(localResultFeatures)
exportMethods(localResultNames)
exportMethods(localResults)
exportMethods(mirrorImg)
exportMethods(origin)
exportMethods(rotateImg)
exportMethods(rotateMinRect)
exportMethods(saveRDS)
exportMethods(scaleImg)
exportMethods(show)
exportMethods(spatialGraph)
exportMethods(spatialGraphNames)
exportMethods(spatialGraphs)
exportMethods(splitByCol)
exportMethods(splitComponent)
exportMethods(toExtImage)
exportMethods(toSpatRasterImage)
exportMethods(toSpatialFeatureExperiment)
exportMethods(transformation)
exportMethods(translateImg)
exportMethods(transposeImg)
exportMethods(unit)
exportMethods(updateObject)
importClassesFrom(BiocGenerics,OutOfMemoryObject)
importClassesFrom(EBImage,Image)
importClassesFrom(SpatialExperiment,SpatialExperiment)
importClassesFrom(SpatialExperiment,VirtualSpatialImage)
importClassesFrom(terra,SpatRaster)
importFrom(BiocGenerics,
  cbind,
  containsOutOfMemoryData,
  saveRDS,
  type,
  updateObject
)
importFrom(BiocNeighbors,
  AnnoyParam,
  KmknnParam,
  findKNN,
  findNeighbors
)
importFrom(BiocParallel,
  SerialParam,
  bplapply,
  bpmapply
)
importFrom(DropletUtils,read10xCounts)
importFrom(EBImage,
  Image,
  clahe,
  closing,
  fillHull,
  makeBrush,
  normalize,
  otsu
)
importFrom(Matrix,
  colSums,
  rowSums,
  sparseMatrix
)
importFrom(S4Vectors,
  "mcols<-",
  "metadata<-",
  DataFrame,
  SimpleList,
  combineCols,
  isEmpty,
  make_zero_col_DFrame,
  mcols,
  metadata,
  setValidity2,
  showAsCell,
  split
)
importFrom(SingleCellExperiment,
  "altExp<-",
  "int_colData<-",
  "int_elementMetadata<-",
  "int_metadata<-",
  "reducedDim<-",
  "reducedDims<-",
  SingleCellExperiment,
  altExp,
  altExpNames,
  counts,
  int_colData,
  int_elementMetadata,
  int_metadata,
  logcounts,
  mainExpName,
  reducedDim,
  reducedDimNames,
  reducedDims
)
importFrom(SpatialExperiment,
  "imgData<-",
  "spatialCoords<-",
  "spatialCoordsNames<-",
  SpatialExperiment,
  addImg,
  getImg,
  imgData,
  imgRaster,
  imgSource,
  mirrorImg,
  rmvImg,
  rotateImg,
  spatialCoords,
  spatialCoordsNames,
  toSpatialExperiment
)
importFrom(SummarizedExperiment,
  "assay<-",
  "colData<-",
  "rowData<-",
  assayNames,
  assays,
  colData,
  rowData
)
importFrom(data.table,
  ":=",
  as.data.table,
  fread,
  is.data.table,
  merge.data.table,
  rbindlist
)
importFrom(grDevices,col2rgb)
importFrom(lifecycle,
  deprecate_warn,
  deprecated,
  is_present
)
importFrom(methods,
  "slot<-",
  as,
  callNextMethod,
  is,
  new,
  setAs,
  setClass,
  setClassUnion,
  setGeneric,
  setMethod,
  setReplaceMethod,
  show,
  signature,
  slot,
  slotNames,
  validObject
)
importFrom(rjson,fromJSON)
importFrom(rlang,
  "!!",
  "%||%",
  .data,
  check_installed,
  is_installed,
  sym
)
importFrom(sf,
  "st_agr<-",
  "st_crs<-",
  "st_geometry<-",
  st_agr,
  st_area,
  st_as_sf,
  st_as_sfc,
  st_bbox,
  st_buffer,
  st_cast,
  st_centroid,
  st_collection_extract,
  st_concave_hull,
  st_coordinates,
  st_covers,
  st_crs,
  st_disjoint,
  st_distance,
  st_drop_geometry,
  st_geometry,
  st_geometry_type,
  st_geometrycollection,
  st_intersection,
  st_intersects,
  st_is_empty,
  st_is_valid,
  st_join,
  st_linestring,
  st_make_grid,
  st_minimum_rotated_rectangle,
  st_multilinestring,
  st_multipoint,
  st_multipolygon,
  st_nearest_feature,
  st_point,
  st_polygon,
  st_read,
  st_sf,
  st_sfc,
  st_simplify,
  st_union,
  st_z_range,
  st_zm
)
importFrom(sfheaders,
  sf_linestring,
  sf_multilinestring,
  sf_multipoint,
  sf_multipolygon,
  sf_polygon
)
importFrom(spatialreg,as_dgRMatrix_listw)
importFrom(spdep,
  card,
  dnearneigh,
  gabrielneigh,
  graph2nb,
  knearneigh,
  knn2nb,
  mat2listw,
  n.comp.nb,
  nb2listw,
  nb2listwdist,
  poly2nb,
  relativeneigh,
  soi.graph,
  tri2nb
)
importFrom(stats,
  aggregate,
  median,
  na.omit,
  setNames
)
importFrom(terra,
  "ext<-",
  as.raster,
  ext,
  inMemory,
  nlyr,
  rast,
  shift,
  sources,
  unwrap,
  vect,
  wrap
)
importFrom(tools,
  file_ext,
  file_path_sans_ext
)
importFrom(utils,
  getFromNamespace,
  head,
  packageVersion,
  read.csv,
  tail
)
importFrom(zeallot,"%<-%")
