Get giotto image object

Get giotto one or more image objects from gobject

Usage

getGiottoImage(gobject, image_type = NULL, name = NULL)

Arguments

gobject

giotto object

image_type

deprecated

name

character vector. Names giotto image object(s) showGiottoImageNames to get

Value

a giotto image object

See also

Other image data accessor functions: setGiottoImage()

Other functions to get data from giotto object: getCellMetadata(), getDimReduction(), getExpression(), getFeatureInfo(), getFeatureMetadata(), getMultiomics(), getNearestNetwork(), getPolygonInfo(), getSpatialEnrichment(), getSpatialGrid(), getSpatialLocations(), getSpatialNetwork(), get_multiomics()

Examples

g <- GiottoData::loadGiottoMini("vizgen")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : 'giotto_env'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/share/miniconda/envs/giotto_env/bin/python"

getGiottoImage(gobject = g)
#> An object of class giottoLargeImage : "dapi_z0"
#> Image extent            : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax)
#> Original image extent   : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax)
#> Scale factor            : 0.108626547903541, 0.10862659908279 (x, y)
#> Resolution              : 9.2058527063567, 9.20584836903386 (x, y)
#> Layers                  : 1 
#> Estimated max intensity : 255 
#> Estimated min intensity : 0 
#> Values                  : integers
#> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Vizgen/VizgenObject/Images/dapi_z0_spatRaster'