BioFormatsImage         On disk representation of BioFormats images in
                        SFE object
BioFormatsImage-getters
                        Other 'BioFormatsImage' getters
ExtImage                Use the EBImage 'Image' class in SFE objects
Img<-,SpatialExperiment-method
                        Image setter
SFE-image               Methods for handling image-related data
SFE-transform           Affine transfortaion of SFE object in
                        histological space
SpatRasterImage         SpatRaster representation of images in SFE
                        objects
SpatialFeatureExperiment
                        Constructor of SpatialFeatureExperiment object
SpatialFeatureExperiment-class
                        The SpatialFeatureExperiment class
SpatialFeatureExperiment-coercion
                        SpatialFeatureExperiment coercion methods
SpatialFeatureExperiment-subset
                        Subsetting SpatialFeatureExperiment objects
addVisiumSpotPoly       Add Visium spot polygons to colGeometry
affineImg               Affine transformation of images
aggBboxes               Aggregate bounding boxes
aggregate,SpatialFeatureExperiment-method
                        Aggregate data in SFE using geometry
aggregateTx             Aggregate transcript spots from file
annotGeometries         Annotation geometry methods
annotOp                 Binary operations for geometry of each
                        cell/spot and annotation
annotPred               Binary predicates for geometry of each
                        cell/spot and annotation
annotSummary            Summarize attributes of an annotGeometry for
                        each cell/spot
bbox,SpatialFeatureExperiment-method
                        Find bounding box of SFE objects
bbox_center             Find center of bounding box
cbind,SpatialFeatureExperiment-method
                        Concatenate SpatialFeatureExperiment objects
changeSampleIDs         Change sample IDs
colFeatureData          Get global spatial analysis results and
                        metadata of colData, rowData, and geometries
colGeometries           Column geometry getters and setters
containsOutOfMemoryData,SpatialFeatureExperiment-method
                        Whether an SFE object contains out of memory
                        data
crop                    Crop an SFE object with a geometry
cropImg                 Crop images
df2sf                   From ordinary data frame to sf to construct SFE
                        object
dim,BioFormatsImage-method
                        Find dimension of BioFormatsImage
dim,ExtImage-method     Find dimensions of ExtImage
dimGeometries           Dimension geometry methods
ext                     Get and set extent of image objects
findDebrisCells         Identify cells in small bits outside the main
                        piece of tissue
findSpatialNeighbors    Find spatial neighborhood graph
findVisiumGraph         Find spatial neighborhood graphs for Visium
                        spots
findVisiumHDGraph       Find Visium HD spatial neighborhood graph
formatTxSpots           Read and process transcript spots geometry for
                        SFE
formatTxTech            Read and process transcript spots for specific
                        commercial technologies
gdalParquetAvailable    Check if Parquet GDAL driver is available
getParams               Get parameters used in spatial methods
getPixelSize            Get physical size of pixels
getTechTxFields         Get relevant fields and file paths for
                        transcript spots
getTissueBoundaryConcave
                        Get tissue boundary from concave hull of cell
                        geometries
getTissueBoundaryImg    Get tissue boundary from histology image
imageIDs                Show all image_ids in the SFE object
imgRaster               Get the image from *Image class
imgSource               Source of images that are on disk
localResults            Get and set results from local spatial
                        statistics
mirrorImg               Mirror/flip images
multi_listw2sparse      Convert multiple listw graphs into a single
                        sparse adjacency matrix
read10xVisiumSFE        Read 10X Visium data as
                        SpatialFeatureExperiment
readCosMX               Read CosMX data into SFE
readSelectTx            Read transcript spots of select genes
readVisiumHD            Read Visium HD data
readVizgen              Read Vizgen MERFISH output as
                        SpatialFeatureExperiment
readXenium              Read 10X Xenium output as
                        SpatialFeatureExperiment
reexports               Functions re-exported from other packages
removeEmptySpace        Remove empty space
rotateImg               Rotate image
rowGeometries           Row geometry getters and setters
sampleIDs               Get all unique sample IDs
saveRDS,SpatialFeatureExperiment-method
                        Save SpatialFeatureExperiment as RDS file
scaleImg                Scale image
show,SpatialFeatureExperiment-method
                        Print method for SpatialFeatureExperiment
spatialGraphs           Spatial graph methods
splitByCol              Split SFE object with categorical vector or
                        geometry
st_any_pred             Simple geometry predicates
toExtImage              Convert images to ExtImage
toSpatRasterImage       Convert images to SpatRasterImage
translateImg            Translate/shift image in space
transposeImg            Transpose images
unit,SpatialFeatureExperiment-method
                        Get unit of a SpatialFeatureExperiment
updateObject            Update a SpatialFeatureExperiment object
visium_row_col          Row and columns of Visium barcodes on the slide
